At a surface level, the conflict at Mercer University this week appears to be about tolerance of gay students. The Georgia Baptist Convention voted Tuesday to sever ties to Mercer, citing the university's decision to let a gay student organization sponsor a session where students could talk about homosexuality.

But whatever some Baptist leaders may have said about Mercer welcoming gay groups, the university actually asked the student group to disband, which it did. So if the Baptists follow through with their plans, they would be punishing Mercer by holding back millions of dollars that provide scholarships for Baptist students -- all because of a student group that existed only briefly and that the university shut down.

If Mercer is enforcing Baptist rules about gay people, why all the fuss? Experts say that there are multiple conflicts going on. To be sure, one concerns gay rights -- a flash point not only at Mercer, but at other Baptist colleges and institutions of other faiths as well. But more broadly, there is the question of who runs Baptist colleges -- state conventions or boards of trustees.

"I think they wanted to defund Mercer University because they couldn't control it," said Rev. David W. Key, director of Baptist studies at Emory University's theology school. Mercer's charter, Key said, limits the convention's control over it, so state officials would prefer to spend their money on colleges that they can control. In fact, the Georgia Baptist Convention waged a long legal battle -- that succeeded this year -- to regain complete control over the board of Shorter College.

At the same time, Baptist colleges with enough financial strength and enough control of their charters to do so are negotiating splits with their state conventions -- giving up money that has come from state conventions but gaining control over their boards in the process. Among institutions going down that road are Belmont University (with the Tennessee Baptists) and Georgetown College (with the Kentucky Baptists). In the case of Belmont, the governance issue came to a head over the university's desire to have some board members be non-Baptist Christians and the state convention's insistence that all trustees be Baptists.

According to Key, "all of them -- all of the Baptist colleges -- if they had the money and legal way of doing it, would pull out tomorrow."

Rev. Jerry Mahan, a Mercer trustee who is pastor of the First Baptist Church, in Moultrie, Ga., agrees. "I think they had their minds made up that they were going to do this way before any of the controversy about that group meeting on campus. That became an excuse for them to use."

Leaders of the Georgia Baptist Convention could not be reached for comment Wednesday, but the resolution calling for an end to ties with Mercer faults the university on a number of grounds -- primarily cases in which the university deviated from "Biblical theology and doctrine," and especially the recent case involving the gay student group.

Gay issues clearly have made Baptist colleges and their state conventions uneasy. The Virginia Baptist Mission Board cut ties to Averett University because that institution allowed a Gay/Straight Alliance to be formed. Baylor University recently kicked an alumnus off the business school's advisory board -- even though he had been a long-time volunteer and donor -- because the institution found out he is gay. And earlier this year, Baylor ordered the campus Starbucks to remove coffee cups that contained a quote from a gay writer.

"There have always been gay students at Mercer and other colleges like that, and the colleges have always been bigoted toward gays, but the gay community is changing," said Jacob Reitan, director of Equality Ride, a group that organizes protests of the anti-gay policies of religious and military colleges. Reitan said that gay Mercer students a decade or so ago would have been hoping to stop being gay, or would have tried to hide being gay, or would have accepted being miserable.

Today, he said, many gay and straight students at religious colleges see being gay as morally equivalent to being born left-handed -- a part of life for some people. So colleges like Baylor or Mercer can no longer count on students accepting anti-gay ideas or rules. He said that colleges that deny their students basic rights such as forming groups or coming out are engaged in "spiritual violence" against their students -- many of whom, Reitan noted, care deeply about their faith.

Baptist groups, Key said, "just feel that there is too much social change," and see gay student groups as being tied up in issues of gay marriage and general challenges to their beliefs. Key went so far as to say that the dispute over gay issues threatens to make it impossible for Baptist groups to be good stewards of colleges.

"Higher education wants to open minds and if you think you have all the truth, you don't want to open minds," Key said. "Fundamentalism is not compatible with higher education."

Nate Mouttet, director of communications for the Council for Christian Colleges and Universities, said that he couldn't speak for Mercer (which isn't a member of his group), but that it was important for people to realize that many religious colleges make known to prospective students and faculty members that certain religious beliefs and conduct are expected of everyone.

"We are aware that most of our member campuses, the majority of which are owned and operated by more than 20 orthodox denominations, will not agree that homosexual practice is consistent with Scripture," he said, in a statement on behalf of the council. "However, our campuses are educational institutions and we hope that they will foster positive dialogue even on areas of disagreement. More importantly we hope that our campuses will be safe and encouraging places as students work through issues of sexual identity."

There are some signs that gay rights groups may be able to have the kind of "positive dialogue" with Christian colleges that the statement refers to. Reitan, of Equality Ride, said that his group had recently accepted the council's invitation to talk about ways that visits to religious colleges could take place in a way that everyone would accept. When the group held an event at Liberty University, organizers were prevented from giving books on gay topics to the library or giving university officials copies of letters from gay students and alumni.

Both Reitan and Mouttet said that the discussions between their groups  -- which hadn't started at the time of the Liberty visit -- have been respectful and that they were hopeful that they could work out a way for the Equality Ride to visit campuses in a way everyone would consider productive.

But at Mercer -- as at many colleges -- the headlines about gay groups being accepted don't reflect the reality of the college's views. Mahan, the trustee and someone designated by the college to speak about the current dispute, said that gay groups have no place at the university. And while he acknowledged that a gay group had sponsored a discussion on campus, he said that Baptist leaders incorrectly said that the group had been allowed to have a "coming out" day.

"We are a Baptist university and I believe that life style is contrary to the will of God," he said. Mahan said that he realized Mercer has gay students, that they are "worthy people," and that he hoped that they would do well academically, and stay celibate. "I believe that sexual relations are reserved for marriage, so single heterosexuals should live a celibate life and homosexuals should live celibate lives," he said.

He said that he would support a gay student group if its sole purpose would be to help gay students be celibate.