Wow! That just stuns me. I know it shouldn't, but the fact that anyone in this day and age thinks they can evict you for not being an xtian is just bizarre to me! I don't know what you could do about it, maybe contact a lawyer?
Talk to a lawyer? Absolutely.
Also, get with the Freedom From Religion Foundation. They've provided serious muscle to cases such as yours multiple times and are very much worth having on your side.
Try to call in to the radio show Your Legal Rights. You can pose a question directly on the air and you can also talk to one of their bank of volunteer attorneys during the show hours. Also check out the Department of Consumer Affairs website section on tenant law. There are a lot of useful links in there, such as local housing advocacy organizations, what constitutes discrimination and what remedies and compensation you may be entitled to if your landlord breaks the law.
A funny reaction I got when asked about my religion, and I replied I'm an atheist:
"Awwwww... I like people like you!"
It wasn't so bad, I guess, but the phrase... People like me? Sounded a bit weird...