As a moderator on a primarily programming forum (
www.realgurus.com), we have had religion threads come up in our off-topic forum occasionally. We don't disallow them, but we watch them very closely, and if they look like they're going to turn into a religion bashing thread, we post "watch out or it's locked". Then, when required, the thread is locked. Usually they just die out on their own.
It's worked really really well for us.
My $0.02...
Dave