How is depriving people of their right to spiritual beliefs any different than depriving someone of their right to marry interracially?
For crying out loud, no one is trying to deprive people their right to their spiritual beliefs.
Most religious people I know actually don't try to force people to conform to their morals and I've met just as many, if not more atheists who are even MORE obnoxious than religious folk in trying to force people to conform to their (lack of) a belief system.
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.
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 perfectly free to pray five times a day at specific times. Trying to force other people to do that too is not okay.
Are we clear?