I just got out of the Army. In fact, I was stationed at Ft. Riley as recently as January 2005 and there was definitely some Christian bias.
For one thing, there were very few religious options available for non-Christians. The only services in the post chapel were Christian and all the chaplains I’ve seen (except for one*) were some denomination of Christianity. I saw local (civilian) Wiccan and Jewish services advertised on a billboard one time in basic training, but that was the only time I ever saw any non-Christian religions even acknowledged. Come to think of it, the only people I ever met who weren’t either Christians or atheists were in basic training. Maybe the Army weeds them out, I don’t know. The only other one I heard of was SGT Akbar who threw that grenade into his CO’s tent in 2003.
*In Iraq once, all the way across a big DFAC, I regognized a Jewish chaplain by his yarmulke and the star of David on his chest.
It seems prayers were almost always held before or after every formation, ceremony --even the races I ran in Iraq were preceded by prayers. I, an atheist, usually just took my hat off and stared blankly into space. I don’t want to disrespect everybody but I don’t want to play along either. All that God-thanking gets pretty irritating after awhile.
In conversation I didn’t lie to anybody, but usually I tried to steer clear of the topic of religion altogether. With the guys I worked with everyday it wasn’t such a big deal to be an atheist. But with senior NCOs and officers, I could see it becoming a problem; that’s why I tried not to let the subject come up, or say something vague if it did. In the Army, unlike the real world, your bosses don’t just tell you how to do your job – they’re pretty much the boss of your whole life.
Most soldiers I knew kept their religious views private. It seemed to me (looking from the outside) like usually there was a small bible-studying first-name-basis-with-chaplain hardcore Christian clique. Then there were the fair weather Christians (the majority) who rotated in and out of this clique in various intervals.
In my experience though, everyone was professional and didn’t let their religious views cloud their judgment at work. It was more of a bias than discrimination. The rules are pretty clear, so that keeps open discrimination to a minimum. It was just the annoying amount of prayers and a seemingly-institutional perception that rocking the boat is a bad thing, regardless of the rules. I can definitely see those ingredients cooking up a situation like the guy in the OP.
As to the questions in the OP, I don’t know if things have changed or if it has always been this way. That’s just my experience.