Write what you want to write. More importantly, write what makes sense for the world you've created. If people don't like it, they don't have to read it. You're writing fiction, not cramming your religious beliefs down someone's throat. I think most readers get that. And unless you're just using your fiction to foist a thinly-veiled presentation of your personal religious beliefs onto your audience, I don't think you're going to have a problem.

Orson Scott Card wrote an interesting treatise on religion in SFF, and I think he makes some good points.

http://www.writing-world.com/sf/card.shtml