For crying out loud, no one is trying to deprive people their right to their spiritual beliefs.
The democratic party in general, and Michael Newdow and the ACLU in particular, are attempting to do so daily.
If you believe that homosexuality is a sin, you are perfectly free to refrain from any homosexual acts. However demanding that other people do that too, or trying to enact laws that discriminate against gays is not okay.
Push them too much, and you're gonna convince a lot of them that it is not only ok, but a good idea, too.
You are perfectly free to believe that instead of evolving from other animals, humans were created by a god. You are perfectly free to believe that instead of being born, babies are brought by storks. However, trying to get public schools to teach those things instead of actual science is not okay.
You are also free to believe in catastrophic anthropogenic warming, disarmament of civilians, prohibition of drugs, public nudity, bans on public nudity, and a variety of other religious or pseudo-religious ideas. But we tolerate that nonsense, too, as no-one has all the answers, and anyone who claims to should be sent to coventry.
You are perfectly free to pray five times a day at specific times. Trying to force other people to do that too is not okay.
Trying to shut up people praying is also not okay. Deliberately inventing a wall of separation between church and state that the founders never intended is not okay.
It's clear you have strong opinions, not yet tempered by experience or wisdom. You need not respect any belief or opinion, but you must respect their right to hold it if you want them to respect your right to hold any particular belief or opinion.
Trying to bring this back to topic, a chaplain as a character makes logical sense to anyone who's ever served, but to a producer, author, or other creator, really only works as a back ground character, or for a main character, as a philosophical counterpoint. To a militant atheist, it is, of course, a heinous idea, but then militant atheists rarely have any tolerance anyway.