Nevertheless, during the past week, the House of Representatives took a step toward barring future trials of Guantanamo detainees, adopting as part of a spending bill to keep the government running a resolution that restricts the use of funds to transfer into the United States or release any non-citizen held at Guantanamo as of January 20, 2009, the start of the Obama presidency.
Attorney General Eric Holder was quick to label the action "extreme and risky" and "unwise."
Writing Senate Democratic Leader Harry Reid and Senate Republican Leader Mitch McConnell, Holder said blocking future civilian trials of Guantanamo detainees is "taking away one of our most potent weapons in the fight against terrorism."
Holder's initial decision a year ago to try five Guantanamo detainees for the Sept. 11 attacks, including professed plot architect Khalid Shaiykh Mohammed (KSM), in the same Lower Manhattan courthouse as Ghailani, has stalled. New York political leaders and the city's police commissioner complained about the security risks and costs, while others objected to treating the accused as criminal defendants instead of war criminals.
Holder recently said the Administration is close to a final decision on whether to pursue a civilian trial on the U.S. mainland, settle for a military commission at Guantanamo, or neither, and just continue to detain the defendants as "enemy combatants" in the war on terror indefinitely.
"It would therefore be unwise, and would set a dangerous precedent with serious implications for the impartial administration of justice, for Congress to restrict the discretion of the executive branch to prosecute terrorists in these venues," Holder told the Senate leaders. "The exercise of prosecutorial discretion has always been and must remain an executive branch function."
Congressman Jerry Nadler, a liberal Democrat whose district includes the world trade center site, opposed the House resolution, telling CBS News Sunday, "Whether KSM should get a civilian trial or a military trial, the Justice Department should decide that."
Nadler, who joined the chorus of reservation about a Lower Manhattan trial, voted against the restrictive House resolution. "It is improper for Congress to make such a decision, or even the White House," he said.
Ghailani's case was widely seen as a test for future high value Guantanamo detainees, and after a month long trial in Manhattan federal court, a jury of six men and six woman convicted him of only one count of 285 deliberated - conspiracy to destroy U.S. property - for his role in the 1998 truck bombings of the U.S. embassies in Kenya and Tanzania.
The jury acquitted Ghailani of four other conspiracies, including al Qaeda's overarching global conspiracy to kill Americans, and of the murders of 224 people killed in the embassy bombings.
While some observers were unhappy with the result, Emily Berman, a fellow with the NYU Law School Brennan Center for Justice, told CBS NEWS, Ghailani's case was "a trial whose legitimacy cannot be questioned, without any security problems, without causing any inconvenience to businesses or residents of the area, and without compromising our constitutional values."
Unless one of the anonymous jurors comes forward to explain, we won't know why the jury failed to convict Ghailani on more counts. Did they accept the defense argument that Ghailani did not know the goals of his friends who were in al Qaeda, whom he helped by acquiring the bomb truck and gas tanks and storing detonators? Did a holdout juror force a compromise verdict? Would the jury's verdict have been harsher had the panel heard that Ghailani acquired TNT for the bombings, an allegation not put in evidence?
Berman suggests the failure to convict on more counts rests with the government's past mistreatment of Ghailani, subjecting him to "enhanced interrogation techniques" in a secret CIA prison overseas between 2004 and 2006, which resulted in the exclusion of a key government witness, Hussein Abebe, a Tanzanian miner who admits selling Ghailani TNT in 1998.
On the eve of trial, U.S. District Judge Lewis Kaplan forced Abebe off the government's witness list, because the government learned of him, as the judge wrote, "only through information it allegedly extracted by physical and psychological abuse of the defendant."
According to FBI reports and a pre-trial hearing where Abebe testified, Ghailani made three to five trips in 1998 to the Tanzania city of Arusha, where he told Abebe he was purchasing explosives for pearl mining off the coast of Somalia. Ghailani has also told a military judge in Guantanamo in 2007 that he thought he was buying soap for washing horses.
After the embassy bombings and seeing Ghailani's face on TV as a wanted man, Abebe testified he realized he was tricked, feared getting arrested, and decided to keep quiet until Tanzanian police tracked him down in 2006.
Kaplan prohibited the jury from hearing Abebe, because, the judge ruled, his identity and location was coerced from Ghailani in violation of the Constitution's Fifth Amendment protection against self-incrimination.
"We must adhere to the basic principles that govern our nation, not only when it is convenient to do so, but when perceived expediency tempts some to pursue a different course," Kaplan wrote.
Would a military judge have allowed Abebe to testify? "It is far from clear," Kaplan wrote, even with its "more forgiving provisions of the rules of evidence."
The Military Commissions Act and the Defense Department's military commissions manual preclude the use of statements obtained by "torture or cruel, inhuman, or degrading treatment" and any evidence derived from them.
For example, a military commission prosecution against Guantanamo detainee Mohammed Jawad, who was accused of attempted murder for allegedly throwing a grenade that badly wounded two U.S. soldiers and their interpreter in a 2002 attack in Kabul, fell apart when the military judge ruled Jawad's signed "confession" was coerced. The U.S. flew Jawad home to Afghanistan.
U.S. Marine Col. Jeffrey Colwell, chief defense counsel on the military commissions who represented Ghailani when he was at Guantanamo, told CBS NEWS, "We too would have moved to have [Abebe's] testimony excluded, for the same reasons counsel did" in New York.
Paul Butler, a prosecutor in the 2001 embassy bombings trial that sent four al Qaeda operatives to life in prison, told CBS News, "It's unclear how a military judge would apply the standard to the facts."
Ghailani faces 20 years to life in prison when he is sentenced next month.
"The guy was convicted of a very serious count and is going away for a long time. The notion that this verdict is a serious loss for the government can be overstated," Butler says.
Butler, who later worked for Defense Secretary Donald Rumsfeld, supported Ghailani's federal trial but favors military commissions for detainees caught after 9/11.
He says the trial was "the perfect wake-up call on the risks of trying these cases in federal courts."
One key difference between trials and commissions is that, unless it's a death penalty case, it takes only a two-thirds majority of a military jury to convict, instead of a unanimous 12-0 vote in federal court. (Military juries need to be unanimous in a death penalty case).
"Military members of a jury frequently hold the government to a higher standard than beyond a reasonable doubt," retired General Thomas Hemingway told CBS News. Hemingway oversaw a review of the military commissions between 2003 and 2007.
"There's nothing wrong with military commissions that public diplomacy and transparency couldn't solve," Hemingway said, adding that plans for trying Guantanamo detainees have improved since the Supreme Court deemed the first tribunals inadequate.
"There are a lot rights available to defendants in a military process that people are unaware of," Hemingway said. "We made seven major rule changes, and all were for the benefit of the accused."
A final conviction in a military commission has the potential to go to the Supreme Court, Hemingway said.
The major difference with trials that favors the government in military commissions is the rule allowing hearsay, second-hand evidence in which a witness describes not what he knows personally, but what someone else has told him.
That's why Hemingway believes Abebe's story about selling Ghailani TNT would have been admissible in a military commission.
If Abebe himself could not testify, an FBI agent who had interviewed Abebe might have related his account.
Charles Stimson, a former federal prosecutor and Navy lawyer (JAG) who oversaw detainee affairs for the Pentagon, also bristles at the criticism of the commissions.
"Those very same groups who are criticizing military commissions are being somewhat disingenuous, because they are not also criticizing the international criminal tribunal of Yugoslavia or the international tribunal of Rwanda or the International Criminal Court, where the rules there are fair less fair to accused than they are in the military commissions," Stimson told CBS News. "In the international tribunals, if the government loses the case, in other words the defendant is acquitted, government can appeal the acquittal. Does that seem fair to most Americans?"
Stimson supports a case by case assessment on the trial vs. commissions debate, but he is clear on where the alleged 9/11 conspirators belong.
"If this is not a war crime that should be tried in military commissions, there really is not a case at Guantanamo that should be tried in military commissions," Stimson says. "If you are going to use commissions - use them. If you're not going to use them, cut those folks free and let them go back to their military jobs."
While federal prosecutors have achieved more than 200 convictions for terrorism-related crimes since 9/11, the military commissions at Guantanamo have yielded only five convictions, all but one through plea bargains, and typically garnered shorter sentences than those imposed by federal judges.
The Brennan Center's Emily Berman said, "If the goal is to convict and incapacitate terrorists, the federal courts seem much more efficient at doing so."
The debate perhaps comes down to the question of whether the proceedings should be measured by their process or their results.
"The perception seems to be that military commissions will more likely reach guilty verdicts. Thus, to insist on the use of military commissions is to disregard the presumption of innocence," Berman said.
General Hemingway said the perception that the only possible result of commissions is convictions is a misunderstanding. "People confuse the fact that the military is disciplined with the idea that you can have rigidity in your disciplinary process," Hemingway said.
When critics of Ghailani's trial suggest he would have been convicted of more offenses by a military commission, that rankles chief defense counsel Jeffrey Colwell.
He says, "It is disturbing if there's a system designed to assure convictions. That's a complete affront to the rule of law."