The situation is complicated, ministers say, because there's a sense that both men have been treated unfairly - and that both have made mistakes.
Many black ministers defended Wright when his more incendiary remarks became an Internet sensation in March, saying context was needed to understand the black church's tradition of challenging injustice.
But Wright lost some of that support after his Monday appearance at the National Press Club in Washington, during which he claimed the U.S. government was capable of planting AIDS in the black community, praised Nation of Islam leader Louis Farrakhan and suggested that Obama was acting like a politician by putting his pastor at arm's length while privately agreeing with him.
The performance was enough for Obama to denounce Wright's comments as "divisive and destructive." That was just six weeks after he portrayed Wright, in a well-received speech on race, as a family member he couldn't disown.
"What I am disappointed in is Rev. Wright's continuing to be in the public eye," said Bishop Charles H. Ellis III, senior pastor of 6,500-member Greater Grace Temple in Detroit. "If he has a point to get across, make your point. We as ministers have to be very careful about our timing."
Another pastor in Detroit - where Wright received a standing ovation Sunday at a dinner for the National Association for the Advancement of Colored People - directed his anger at the Democratic senator.
The Rev. William Revely, pastor of 300-member Holy Hope Heritage Church, questioned Obama's truthfulness in claiming he had not heard some of Wright's contentious remarks from the pulpit.
"Anybody who has heard Jeremiah preach has heard that," said Revely, who has known Wright since the 1970s. "Jeremiah, he's a pastor, and as a pastor you have to see things as they are. Politicians see things as they want them to be."
The punches and counter-punches thrown by Obama and Wright are leaving black churchgoers angry at both, said the Rev. Bennie Whiten, a retired United Church of Christ minister.
People want to embrace Obama's candidacy but worry about recent stumbles and wonder whether he fully understands racial divides still exist, Whiten said. They admire Wright but question his timing and tone.
"I think we've got two very good men, two very strong men, who find themselves in an almost impossible situation from which neither can extricate himself," said Whiten, who lives in Chicago and has worshipped as a visitor at Trinity United Church of Christ.
The Rev. Herbert H. Lusk II, a conservative black pastor at Greater Exodus Baptist Church in Philadelphia, expressed sympathy for Wright but said he relates more to Obama. He compared Obama's situation to his own, as a Republican pastor of an overwhelmingly Democratic congregation. His members get angry over his support for President Bush but remain because of family, friends and other ties, Lusk said.
Obama "doesn't appear to me to be hypocritical or disingenuous," Lusk said. "He's just another parishioner who struggles with what happens in his church, what the pastor says and all the other intangibles."
Wright's Press Club performance forced Obama's hand, said the Rev. Byron Williams, a pastor and columnist in Oakland, Calif. Here was a candidate who built a movement on the notion of America's better self, yet he was being defined by his pastor's rhetoric.
Wright is savvy enough to know that anything positive said about Farrakhan - known for past anti-Semitic remarks - will be portrayed negatively in a 24-hour news cycle, Williams said.
Yet Obama's public rejection of his pastor carries risk. In February 2007, Obama abruptly disinvited Wright from delivering the invocation at the kickoff of his presidential campaign. That move suggests Obama has long known Wright could be a liability and only disowned him when forced, Williams said.
"He is going to have to account for what is perceived as this air of disingenuousness," Williams said.
The Rev. Dwayne A. Walker also confessed to mixed emotions over the rift between Obama and Wright.
Walker, pastor of 1,000-member Little Rock AME Zion Church in Charlotte, N.C., said he admires both men. Yet he understands why Obama broke ties with the minister who helped lead Obama to Christianity, married him and baptized his children.
Walker said what angers him most is how Obama, unlike other presidential candidates, has been defined by what someone else has said rather than by his own words and record.
"Overall, I don't think Obama should be defined by his pastor, nor should Dr. Wright be defined by that moment," he said of the Press Club exchange. "It was a bad moment, and it came at a bad time."
As a pastor, Walker said he has another wish: that politician and pastor eventually reconcile.