Whenever gay and lesbian people exercise the temerity to be treated like real human beings, to have equal employment in the private sector as well as in the military, the right wing religious reaction is always the same -- should they "obey God or obey men."
In the military, the answer is quite clear: they are to obey military code, period. Otherwise, they won't remain military chaplains for long. If President Obama makes good on his promise to repeal Don't Ask, Don't Tell, a group of conservative Christian chaplains expressed their fear in a letter to the president and Defense Secretary Robert Gates that they'll "face a reduction in the free exercise of their faith."
The chaplains use the letter to lodge a litany of complaints about how they'll be forced to compromise their beliefs, how they will have to work with gay people, counsel gay people, and perhaps even conduct a service with gay or lesbian clergy. All of this, they say, means they'll have to condone something they sincerely feel is sinful. I'm certain that the same arguments were made when the armed forces were integrated. Chaplains then -- some who fully believed that simply being black was a sinful state -- had to work with black people, counsel black people, and perhaps even conduct a worship service with black clergy.
http://www.religiondispatches.org/blog/2519/conservative_military_chaplains_fight_repeal_of_dadt_/