I'm a "mainstream Christian" (sorta) and I also find this subject difficult. No matter what, you're probably going to offend someone. I suggest, as others have, to show it through actions rather than words. I also suggest that you focus on religion not as a whole, but as very individual to each character. Perhaps THIS character views going to church every Sunday and participating in bible studies, etc., as necessary to HER spiritual and mental health. Perhaps THAT character values helping others. Everyone's faith, even if we believe similar things, is expressed in a different and unique way. Each of our relationships with God is different-- so don't generalize. Personalize. That way, when others look at your work, no matter what perspective they are coming from, they are unlikely to be offended. They'll see the characters as individuals rather than a statement about this or that religious practice.
I have a character who I "know" is a Christian. But her religious practices don't have anything to do with the story, so I don't mention them. However, towards the end, the reader finds out that her parents were missionaries. I hope that, based on her previous actions, the reader will think, "Hm, that makes sense."