The chaplain, Col. Timothy Wagoner, is remaining on active duty and has affiliated with the Cooperative Baptist Fellowship, which holds more moderate views on homosexuality and some other issues than the Southern Baptists.
"I find very little that is more important and nothing that is more exhilarating than providing for the religious freedoms and spiritual care of all service members and their families — and will joyfully continue to do so," Wagoner said Friday in an email to The Associated Press.
Wagoner's exit from the Southern Baptist Convention, which SBC leaders welcomed, is a direct fallout from the repeal a year ago of the "don't ask, don't tell' policy that had prevented gays and lesbians from serving openly in the military.
Gays are now able to be open about their relationships, and same-sex civil union and marriage ceremonies can take place at military installations if they are legal under state law. New Jersey recognizes civil unions, and thus the June 23 ceremony uniting Tech. Sgt. Erwynn Umali and civilian Will Behrens had legal stature.
Wagoner — the senior chaplain at Joint Base McGuire-Dix-Lakehurst — had made clear he would not officiate at such ceremonies, which the Southern Baptists do not condone.
However, Wagoner had told The AP — in an interview a few days after the ceremony — that he decided to attend as a show of support for the base community, for Umali, and for the Evangelical Lutheran chaplain, Col. Kay Reeb, who presided over it.
"I wouldn't miss it," Wagoner said, describing the ceremony as beautiful.
On July 13, a week after the AP story appeared, the Southern Baptists' official Baptist Press news service ran an article conveying the message that South Baptist military chaplains do not support same-sex civil unions or marriages.
It quoted Wagoner as saying, "''My intention was never to embarrass or misrepresent the Southern Baptists, whom I have faithfully served for 30 years as a pastor and military chaplain."
On July 20, another Baptist Press article appeared, announcing that Wagoner was leaving the Southern Baptist Convention.
It quoted Kevin Ezell, president of the SBC's North American Mission Board, as saying, "When it comes to what our chaplains believe and practice, we do ask and we do expect them to tell."
"We only want to endorse chaplains who can support Baptist doctrine and belief without reservation," Ezell said. "If an SBC chaplain concludes he cannot conduct his ministry in harmony with SBC beliefs and doctrine, then it is best to part ways."
The U.S. military requires that all of its chaplains have the endorsement of an established faith group. According to recent Pentagon figures, the Southern Baptists are the largest endorser — accounting for 450 of the roughly 2,930 active-duty chaplains.
Professor David Key, director of Baptist Studies at Emory University's Candler School of Theology, predicted that Wagoner's departure from the Southern Baptists might be the first of many as their chaplains try to reconcile conflicting loyalties.
"The SBC has been defined by its anti-gay stance," Key said. "They now find themselves not just out of synch with growing segments of society but also out of synch with the U.S. military."
"This may be the beginning of a wave of resignations," Key said. "Showing affirmation for gay and lesbian soldiers is what the military wants, and exactly what the SBC doesn't want. At the moment, it's irreconcilable."
Pentagon guidelines say that chaplains are entitled to adhere to the specific beliefs of their faith, but also should show respect for those who hold different beliefs.
"Air Force chaplains serve airmen of all backgrounds, of all faiths or no faith," said Maj. Joel Harper, an Air Force spokesman.
The Southern Baptists' executive director for chaplaincy, former Army Chief of Chaplains Douglas Carver, was quoted by Baptist Press as calling military chaplaincy "one of the toughest ministries in the Kingdom of God" — in part because of the emphasis on multifaith, multicultural diversity.
"It's a vague environment out there, especially as our chaplains promote and defend the whole counsel of God in a post-'don't ask, don't tell' military environment," Carver said. "Our chaplains are navigating through uncharted waters, where the cultural values of the military increasingly conflict with the traditional values and beliefs of Southern Baptists."
Another retired Army chaplain, Ron Crews, said Wagoner's actions had "dishonoured Southern Baptist traditions" and praised the SBC for maintaining its stance against same-sex unions. Crews is executive director of the Chaplain Alliance for Religious Liberty, a coalition of retired chaplains and other religious leaders which has warned that repeal of "don't ask, don't tell" would lead to conflicts for some chaplains from faiths that disapprove of same-sex relationships.
At the civil union ceremony, Wagoner met several gay rights activists who were in attendance, including Fred Sainz of the Human Rights Campaign and West Point graduate Sue Fulton of OutServe, which represents gay and lesbian military personnel. Both described Wagoner as warm and gracious.
The co-director of OutServe, Air Force 1st Lt. Josh Seefried, is stationed at Wagoner's base and encounters him frequently.
"Chaplain Wagoner is one of the nicest, most sincere people I have met in my life," Seefried said in an email. "He deeply cares for his job and all of us that interact with him.... He embodies the best of the chaplain corps."
David Crary can be followed on Twitter at http://twitter.com/CraryAP