He concurred with the estimates that only a handful of chaplains have left the military because of the repeal. He said "two or three" Catholic chaplains had resigned their commissions in recent months, and guessed that repeal may have been a factor though they didn't cite that specifically.
Another conservative denomination with a large contingent of chaplains — 114 on active duty — is the Assemblies of God.
Scott McChrystal, a retired Army chaplain who oversees them, said the concerns that preceded repeal had not been borne out.
"Since the actual repeal, I cannot recall a single instance where I've gotten a call from one of our chaplains who's had a problem," he said. "Our goal as an organization is simply to provide as much help as we can to anybody we can."
Likewise, Frank Clawson, director of military relations for the Church of Jesus Christ of Latter-day Saints, said none of the 42 active-duty Mormon chaplains with whom he works has reported problems linked to the repeal or expressed a desire to leave the service.
Yet Clawson remains wary that the military could become increasingly inhospitable to religious conservatives.
"I don't know if the vote is in yet," he said. "The pendulum has swung the other way, to where if you do have a faith, you're almost looked down on."
The loudest assertions that conservative chaplains face problems come from outside the active-duty ranks, notably from a coalition of retired chaplains and other religious leaders called the Chaplain Alliance for Religious Liberty. In a letter to a Republican congressman in March, the alliance contended that repeal has been implemented "with an open and palpable hostility" to chaplains and service members who disapprove of homosexuality.
The alliance supports a measure backed by House Republicans that would ban the use of military chapels for same-sex weddings and other similar ceremonies. The Pentagon says it will allow such ceremonies when in accordance with state law.
The alliance's executive director, retired Army chaplain Ron Crews, says some active-duty chaplains are dismayed by repeal-related changes but don't speak out publicly because they fear retaliation or do not get permission from superiors.
However, Crews agreed that few chaplains have left the military because of the repeal.
"We've been encouraging our chaplains to stay the course — we don't want to see an exodus," Crews said. "Some of my chaplains have stated they are going to stay, but they realize there may come a day where they may have to choose obedience to God or their career, and they're going to choose their obedience to God."
With an eye toward the future, when the military community is likely to include more same-sex couples, Crews' alliance has drawn some lines in the sand for chaplains from its affiliated denominations: no role in any ceremony for same-sex couples, no jointly presiding over religious services with gay or lesbian chaplains, no pre-marriage or marriage-strengthening counseling to same-sex couples.
Wagoner suggested there were "no hard answers" to some potential dilemmas, such as if a conservative chaplain objected to participating at a marriage retreat that included a same-sex couple. Perhaps a substitute chaplain could be found, or perhaps the gay couple could pick another date for a retreat, Wagoner said.
"Think of it as an experiment," Wagoner said of the post-repeal era. "It's evolving."
The chaplain coordinators for some relatively liberal denominations suggested that the Chaplain Alliance and its allies are exaggerating the impact of repeal for political purposes.
"They are grasping at straws, in terms of getting something substantial to counteract the repeal," said the Rev. Stephen Boyd of the United Church of Christ, which has about 18 active-duty chaplains and was an early supporter of same-sex marriage.
Bishop James Magness, the coordinator for about 75 active-duty and reserve Episcopal chaplains, said he'd heard a common, positive verdict about repeal from his more conservative Catholic, Mormon and Southern Baptist colleagues.
"The whole argument about religious liberty is so incredibly uninformed, and inflamed by some of the very conservative legal groups," Magness said. "In reality, there's been very little if any of the services forcing any ministerial activity on a chaplain against his or her will."
Chaplain Linsky said he'd respect any chaplain who did leave the military out of principled objections related to the repeal, but knew of no such instances thus far.
"The chaplain corps," he said, "has navigated this issue with great calm and prudence."
Pentagon guidelines: http://1.usa.gov/MFrOTi
Chaplain Alliance for Religious Liberty: http://chaplainalliance.org/
David Crary can be followed on Twitter at http://twitter.com/CraryAP