Although Gen. David Petraeus (at left) is not answering questions ahead of his Senate confirmation hearing next week, his spokesman sent me an e-mail which said, "one of the areas of focus will be in improved Civ-Mil (civilian-military) relations and unity of effort." That might sound like gobbedlygook -- but in the wake of the Rolling Stone fiasco it makes perfect sense.

The disparaging comments that Gen. Stanley McChrystal and his staff made about civilian members of the President's Afghan team revealed real divisions about Afghanistan. You don't have to go all the way to Kabul to hear military officers complain about the bull-in-a china-shop ways of Richard Holbrooke, the President's Special Representative for Afghanistan and Pakistan.

And McChrystal is not the only four star general who complains about Karl Eikenberry, the American ambassador to Afghanistan. McChrystal and his staff were expressing opinions held by many military officers. Their sin was to express them in such an indiscreet and disrespectful way.

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When President Obama announced late last year he was deploying 30,000 additional troops to Afghanistan, he said the troop surge would "allow us to begin the transfer of our forces out of Afghanistan in July of 2011."

But it's become increasingly clear that the July 2011 deadline is more about politics than policy.

That's true for a few reasons. First off, the president said from the beginning that July 2011 was only when forces would begin to be brought home - which means he could conceivably bring back just a few thousand troops and still technically meet the deadline.

But more importantly, the White House and military have made clear the deadline can simply be changed depending on conditions on the ground. Adm. Mike Mullen, the chairman of the Joint Chiefs, said Thursday that if the strategy doesn't look like it's working at the end of the year, the military may recommend that the timeline be altered.

Defense Secretary Robert Gates, meanwhile, stressed that the drawdown plan is "conditions-based," and said while General David Petraeus agrees with the president's overall strategy, "when he gets on the ground, he will assess the situation for himself."

"And at some point, he will make recommendations to the president," Gates said. "And that's what any military commander should do. And the president will welcome those recommendations. But at the end of the day, the president will decide whether changes are to be made in the strategy."

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President Obama today said he has full confidence in Gen. David Petraeus, the new head of U.S. forces in Afghanistan, to carry out his administration's strategy there. The president insisted the strategy will stay the same, and for now, so will his top civilian leaders in Afghanistan.

"We are in the midpoint of implementing the strategy we came up with last year," Mr. Obama said with respect to the war in Afghanistan. "Gen. Petraeus understands that strategy because he helped shape it. My expectation is he will be outstanding in implementing it, and he will not miss a beat because of the change in command in the Afghan theater."

The president said that part of the reason he is confident Petraeus will successfully carry out the strategy in Afghanistan is that Petraeus "helped write the manual for dealing with insurgencies" and is also intimately familiar with the players on the ground.

Mr. Obama yesterday nominated Petraeus to replace Gen. Stanley McChrystal in Afghanistan, after McChrystal made disparaging remarks about the administration in a Rolling Stone article. Lawmakers have promised Petraeus a quick confirmation process, but some are planning to press the general on the administration's intentions of beginning a draw down of forces in July 2011.

"We did not say that starting July 2011 suddenly there would be no troops from the United States or allied countries in Afghanistan," Mr. Obama said today. "We said we'd begin a transition phase in which the Afghan government is taking on more and more responsibility."

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Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff, said today that he was "nearly sick" when he read the Rolling Stone article that led to the resignation of Gen. Stanley McChrystal from his role as top commander in Afghanistan.

"Literally, physically, I couldn't believe it," he said. "...I was stunned."

Mullen was joined at a press conference with Defense Secretary Robert Gates where both men expressed support for President Obama's decision to accept McChrystal's resignation.

"I cannot excuse his lack of judgment with respect to the Rolling Stone article or a command climate he evidently permitted that was at best disrespectful of civilian authority," Mullen said, after lavishing praise on McChrystal for his service. "We do not have that luxury, those of us in uniform."

"We do not have the right, nor should we ever assume the prerogative to cast doubt upon the ability or mock the motives of our civilian leaders, elected or appointed," he continued. "We are and must remain a neutral instrument of the state, accountable to and respectful of those leaders, no matter which party holds sway or which person holds a given office."

Gates said McChrystal used "poor judgment" that "made his continued service in that post and as a member of the national security team untenable."

"Our singular focus must be on it succeeding in this mission without distraction or division," he said. "...This is the best possible outcome to an awful situation."

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Now that President Obama has ousted Gen. Stanley McChrystal from his role as head of U.S. forces in Afghanistan, some lawmakers and political pundits are saying the president should continue cleaning house and replace U.S. Ambassador Karl Eikenberry and Special Representative to Afghanistan Richard Holbrooke.

Mr. Obama yesterday announced he was replacing McChrystal with Gen. David Petraeus in the wake of derisive comments McChrystal and his staff made about numerous members of the administration to Rolling Stone magazine -- including Eikenberry and Holbrooke. The article revealed a dysfunctional relationship between the civilian and military sides of the Afghanistan team.

Sen. John McCain said this morning on ABC's "Good Morning America" that he told Mr. Obama more personnel changes are needed to right the ship.

"We need a new team over there as well, perhaps at the embassy and other areas," he said. "The relationship between civil and military is not what it should be."

Sen. Kit Bond (R-Mo.) made similar statements today on Fox News' "Fox and Friends."

Asked whether Mr. Obama should replace Eikenberry and Holbrooke and "muzzle" Vice President Joe Biden on the issue of Afghanistan, Bond said, "That would be a good start."

"That's the kind of plan that I hope the president was referring to yesterday when he said we must have the entire team working together," he added.

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Updated at 11:05 a.m. ET

Senate leaders have promised Gen. David Petraeus a swift confirmation next week so he can assume his new role as head of U.S. forces in Afghanistan, but not before questioning him about President Obama's pledge to begin withdrawing troops in July 2011. Some are also calling for additional personnel changes in the Afghanistan team.

"The issue that will be raised in General Petraeus' confirmation hearings is exactly what is meant by withdrawal in the middle of 2011, whether that is, 'etched in stone,' as the president's spokesperson, Mr. Gibbs, stated or whether it will be conditions-based," Sen. John McCain said yesterday in a press conference. "We feel very strongly that it needs to be condition- based, because if you tell the enemy when you are leaving, then obviously it has an adverse effect on your ability to succeed. So that is a major concern. And there's still a great deal of ambiguity about that issue."

McCain reiterated his concern this morning on ABC's "Good Morning America. (Watch the video below)

"We cannot tell the enemy when you are leaving in warfare and expect your strategy to be able to prevail," he said. "That's just a fundamental of warfare."

McCain also said he told the president that he should make further personnel changes.

"We need a new team over there as well, perhaps at the embassy and other areas," he said. "The relationship between civil and military is not what it should be."

During yesterday's press conference, Sens. Lindsey Graham (R-S.C.) and Joe Lieberman (I-Conn.) backed up McCain's assertions.

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Though he never served in the military, President Obama today served notice on Pentagon brass that he's a tough Commander-in-Chief with zero tolerance for comments that undermine his authority or policies.

In relieving Gen. Stanley McChrystal of command in Afghanistan, Mr. Obama said he wasn't acting "out of any sense of personal insult" for the critical comments attributed to McChrystal and unnamed aides in the new issue of Rolling Stone.

"The conduct represented in the recently published article does not meet the standard that should be set by a commanding general," the president said in a Rose Garden statement.

In his view, "it undermines the civilian control of the military that is at the core of our democratic system." In other words, as Commander-in-Chief, he demands respect and not a hint of insubordinate language, much less conduct.

Ironically, parts of Mr. Obama's 8-minute statement sounded more like a lavish tribute to Gen. McChrystal, not an explanation of why he was being fired.

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Congressional lawmakers on both sides of the aisle reacted positively to President Barack Obama's decision for a change in command in the Afghanistan war.

"I have great respect for General McChrystal and the job he's done in Afghanistan and elsewhere in service of our country, but I respect the decision of our Commander-in-Chief," said House minority leader John Boehner in a statement.

Most Republicans echoed that statement in a rare show of support for the president. Many said that while understandable, it's unfortunate that the respected General Stanley McChrystal had to resign after showing disrespect for the president in a Rolling Stone article.

Sen. Lindsey Graham (R-S.C.) said at a press conference this afternoon that the president "had no other choice" to successfully preserve the chain of command with civilian control over the military. "We lost a good general, but the president, in my view, had no other choice, because to keep him there would have blurred a line that served this country very well for a very long time."

The other area of rare agreement on Capitol Hill was praise for Mr. Obama's choice of Gen. David Petraeus to take over as the top commander in Afghanistan. Lawmakers have great respect for the general after he successfully led the "surge" in Iraq.

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General Stanley McChrystal walked into the Oval Office at 9:51 a.m. today and promptly offered President Obama his resignation as Commander, U.S. Forces in Afghanistan. Mr. Obama, who had already discussed replacing McChrystal with General David Petraeus according to administration officials, accepted McChrystal's resignation.

But we're told their one-on-one meeting lasted for about 30 minutes. So here's the question the White House isn't answering: if the president was already thinking about McChrystal's replacement, what did the two men discuss for half an hour?

Did McChrystal make an argument to keep his job? Was the president reluctant to fire him?

So far, at least, the usual suspects among White House officialdom aren't saying. And maybe they don't know. They weren't in the room.

It wasn't until after his meeting with McChrystal that the president called in his top National Security advisers: Vice President Joe Biden, Secretary of Defense Robert Gates, Secretary of State Hillary Clinton, Chairman of the Joint Chiefs of Staff Admiral Mike Mullen, National Security Adviser James Jones and Chief of Staff Rahm Emmanuel. The president told them that he intended to appoint General Petraeus to take over in Afghanistan.

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President Obama today replaced Gen. Stanley McChrystal with Gen. David Petraeus, one of the few generals believed to be capable of smoothly taking over the war in Afghanistan.

The war effort was complicated this week by the release of a shocking article in Rolling Stone magazine in which McChrystal and his staff members made a number of derisive comments about the Obama administration. By putting Petraeus in charge, however, Mr. Obama reaffirmed his commitment to a war strategy that Petraeus played a central role in shaping.

"This is a change in personnel but it is not a change in policy," the president said.

The 57-year-old general, as the head of U.S. Central Command, was McChrystal's boss and oversaw both the wars in Afghanistan and Iraq. Before taking that role, he served as the top coalition commander in Iraq, where he won wide praise for overseeing the "surge" strategy. The strategy was perceived as a success as violence fell in Iraq and the U.S. was able to develop its plans for leaving the country.

Petraeus also critically brings with him key relationships with political and Pakistani leaders, the Atlantic's Max Fisher reports.

Sen. John Cornyn (R-Texas) today hailed Petraeus as a "tried and true field commander and the architect of modern counterinsurgency strategy."

Petraeus' high-profile career has made him one of the most well known generals of his generation and a recipient of widespread praise. He has been considered a strong candidate to be the next chairman of the Joint Chiefs of Staff, and some have speculated that he will run for president.

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In announcing that he was replacing General Stanley McChrystal with General David Petraeus as the top commander in Afghanistan, President Obama made clear that while there would be a different man at the top, the war strategy would remain exactly the same.

"This is a change in personnel but it is not a change in policy," the president said in the Rose Garden, stressing that Petraeus, as the commander of U.S. Central Command, "supported and helped design the strategy we have in place."

Mr. Obama pointedly stated that he was removing McChrystal because derogatory comments by the general and his staff - conduct that he said "does not meet the standard that should be set by a commanding general" - and not because of "any difference in policy with General McChrystal, as we are in full agreement about our strategy."

But it's important to realize that the most important part of the Rolling Stone article that brought down McChrystal may not have been the incendiary quotes but rather the complaints from the military rank and file that the strategy isn't working.

Policies about limiting civilian casualties have soldiers complaining they can't effectively fight; one showed author Michael Hastings a card with regulations including "Patrol only in areas that you are reasonably certain that you will not have to defend yourselves with lethal force."

Said the soldier: "You sit and ask yourself: What are we doing here?"

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Gen. Stanley McChrystal was ousted by President Obama on Wednesday as the top U.S. general in Afghanistan.

Following Mr. Obama's Rose Garden remarks announcing the move, McChrystal released a statement saying he still "strongly" supports the mission in Afghanistan and that he resigned "out of respect for this commitment" and "a desire to see the mission succeed."

The full statement is below:

This morning the President accepted my resignation as Commander of U.S. and NATO Coalition Forces in Afghanistan. I strongly support the President's strategy in Afghanistan and am deeply committed to our coalition forces, our partner nations, and the Afghan people. It was out of respect for this commitment -- and a desire to see the mission succeed -- that I tendered my resignation.

It has been my privilege and honor to lead our nation's finest.

More Coverage:

McChrystal Relieved of Duty; Petraeus Tapped
Watch Obama's Statement
David Petraeus Brings Experience to the Job
What Happened in the Oval Office
In Afghanistan, a New General -- But An Old Strategy
Bob Schieffer and Bill Plante React to the Announcement
McChrystal Statement: I Resigned to See the Mission Succeed
McChrystal Situation Imperils War Funding Bill
Washington Unplugged: McChrystal Fallout Shakes Up Administration
Is McChrystal "Damaged Goods"?
Pictures: General McChrystal and President Obama
CBSNews.com Special Report: Afghanistan

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Passing an emergency war funding bill to pay for President Obama's 17,000 troop increase and continued efforts in Afghanistan was never going to be easy in the House. Liberals are weary of war, fiscal hawks are concerned about deficits and Republicans are increasingly willing to vote against troop funding if Democrats lard up the bills with measure that have nothing to do with war.

Democratic aides say that Gen. Stanley McChrystal made things a little more complicated. That funding is to pay for the execution of McChrystal's strategy. For his vision. One leadership aide said that the shocking profile of McChrystal in Rolling Stone raised serious questions about McChrystal's judgment and leadership at a time when they are struggling to get Democratic votes for the money. Now, the general has been relieved of duty and replaced by Gen. David Petraeus.

One Democratic aide said that deciding on the best way forward is complicated by members' belief that Republicans will just say no to everything so Democrats have to find ways to pass things with just Democratic votes. The aide said "it's like putting together a puzzle without a picture."

When asked what needs to happen for Republicans to support the bill, House minority leader John Boehner said this morning that he's "hopeful that the Democrat majority in Congress bring a clean supplemental to the floor of the House so that members can cast their votes."

60 Minutes: Stanley McChrystal

Democratic leadership aides said that they are still looking at a number of options to try to pass a supplemental bill that Defense Secretary Robert Gates says is needed by the July 4th recess:

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Aides to Gen. Stanley McChrystal say he wants to keep his job because he can't stomach the thought of abandoning the mission in mid race.

He met with Defense Secretary Gates and Chairman of the Joint Chiefs Mike Mullen this morning for 30 minutes and is waiting to be summoned to the White House. We won't know his fate for a few more hours, but whether or not he loses his command he has already lost something just as valuable to him - his reputation as a good soldier.

Inside the military, there is nothing unusual about exasperation with civilian leadership, which always has larger objectives than the battle in front of them, but displaying contempt runs counter to everything an officer is taught from the day he shows up at West Point.

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