When i was in the Arny, in my third year, i had occasion to go pick up my personnel record, and i noticed that my religious preference had been "whited out" and "non-christian" had been typed in. I went to the clerk responsible, a civilian employee and as it turned out, a rabid fundamentalist, and complained, and he basically told me to blow it out my . . .
So, i went to the officer responsible for his section. He went to this clown, and insisted he change the entry, and when the guy refused to do so, he sent him home that day without pay (or so he said in my presence), and had another member of his section retype the form from scratch, and put "Druid" in the appropriate blank. I had found out that as nobody in the Arny knew anything about Druids, i could pretty well tell them anything i wanted. I told them that my sabbath was from sundown Friday until sundown Saturday, and that i had to go to a grove of oak trees or pine trees. They bought it (probably because it was easiest just to go along), and ever after, i was excused duty from six p.m. on Friday until six p.m. on Saturday.
Jews and oddballs like me were always asked to do duty on christian holidays, such as Christmas or Easter, and to make the request attractive to us, we were always given two days off for each day we were on duty (sort of the Arny equivalent of double time for holidays). I took full advantage of it.
But there is no mechanism in the armed forces for dealing with the religious crackpots if they do get out of hand. When i was in a surgical hospital overseas, the NCO in my section once sneered that you couldn't even get a decent christmas tree from these "gooks." I pointed out that as they weren't christians (the majority were Buddhists), that shouldn't be a surprise. He went mental on me, and recommended that i be put up on charges. The detachment commander (a hospital has a commander, who has to be a surgeon, but the NCOs and enlisted men are members of the medical detachment which has its own commander, usually a lieutenant) happened also to be a christian crackpot, and he took two thirds of two months pay from me via Article 15, for blasphemy (i **** you not). The hospital commander was a surgeon, and a major, and his only response to me complaining was to wring his hands and say "Oh Dear" in so many words. However, the executive officer was a Lieutenant Colonel, with over 30 years service, and he absolutely hated my section commander (the holy roller NCO) and delighted in tormenting the detachment commander. He took me aside, and carefully explained to me the provisions an article of the UCMJ which allowed me to file a protest with any officer, which would then have to be forwarded to the Department of the Army, through the chain of command. So, i filed a complaint with him.
My NCO ended up in a battalion aid station (i suspect his fatigue pants turned brown, he had assiduously avoided any duty which might take him in harm's way), and the detachment commander was censured in front of the entire detachment by the hospital's executive officer, who very obviously took great delight in the exercise.
All of that being said, there have been allegations in the last few years that fundamentalist christians have attempted to take over the Air Force Academy.
Air Force Sued Over Religion (CBS News)
That suit was brought by a Jew who graduated the academy and recounted episodes of anti-Jewish rhetoric among cadets, as well as fundamentalist proselytizing. Weinstein's father was a graduate of the United States Naval Academy, and his oldest son and his daughter-in-law are both graduates of the Air Force Academy. His youngest son is now attending the Air Force Academy. Weinstein has founded a watchdog group, and claims that 4000 currently serving members of the armed forces have contacted him with claims that they were pressured to convert to christianity, or to the fundamentalist doctrine of certain chaplains.
Air Force Removes Chaplain from Post (the Washington Post)
Captain MeLinda Morton, a 13 year veteran of the Air Force, and formerly executive officer of the chaplain unit at the Academy, also alleged a fundamentalist atmosphere at the Academy.
DENVER, May 12  -- An Air Force chaplain who complained that evangelical Christians were trying to "subvert the system" by winning converts among cadets at the Air Force Academy was removed from administrative duties last week, just as the Pentagon began an in-depth study of alleged religious intolerance among cadets and commanders at the school.
"They fired me," said Capt. MeLinda Morton, a Lutheran minister who was removed as executive officer of the chaplain unit on May 4. "They said I should be angry about these outside groups who reported on the strident evangelicalism at the academy. The problem is, I agreed with those reports."