books with religious themes

I don't think featuring god and the devil and assorted angels and demons makes a good book a harder sell. I DO think if you use those characters to tell an intriguing story you can succeed. But if you use those characters to make a point, like "Christianity is right!" or "Christianity is wrong!" then you probably won't succeed. (Except a "Christianity is right!" book can succeed in the Christian lit market obviously)

I LOVE "The Book of Joby" by Mark Ferarri. Basically The Book of Job plus King Arthur=WIN. For more fun with the book of Job, there's also "Job: A Comedy of Justice" by Robert Heinlein.

There's a short story by Arthur C. Clarke called "The Star". It's very well-loved. Lord of Light by Roger Zelazny is about Hindu deities and Buddhist figures (sorta).

Also read this: http://en.wikipedia.org/wiki/Religious_ideas_in_science_fiction
http://en.wikipedia.org/wiki/Religion_in_speculative_fiction

Actually even in Christian publishing if the book is too beat you over the head with its message, especially if you are trying to market it as sci-fi/fantasy it won't succeed no matter what that message is.

Our very own Jay L. Young (III) Hero's series

It's described as "The X-Men meet the new testament".

It's awesome.

That is all.

"Sparrow" by Mary Doria Russel
The Hyperion Cantos by Dan Simmons

In answer to 2) The most important thing is writing a good book, whatever that means to your audience and narrative needs. If you anger people, getting banned by religious groups is good PR. If you please people, word of mouth is the best marketing tool.

Worrying about issues other than quality is often the road to writer's block. Focus on telling the best story you can. You can fix anything else later.

Check out "Lamb" by Christopher Moore for a look at how Jesus might have been exposed to Buddhism and kung fu.

See basically anything by Gene Wolfe.