My favorite in this vein is the Incarnations of Immortality series by Piers, "Pantheon? It's just a job," Anthony.
I suppose my favorite author overall for presentation of religious themes in a fictional setting would be Graham Greene. His writing is drenched with in the trenches practicality of religious practice over sanctimonious externalities. Greene tends to show good or evil as being distant bureaucratic echoes of the human condition found throughout the world, and of lesser importance. What really matters is the immediate: the struggle with what is right or wrong.
Greene is extremely good at hitting the reader with the full force of just how wrong a single situation or event can be.
My favorite novel depicting a fictionalized religion is Messiah by Gore Vidal. While fictional, the movement (with punning intentionality) named Cavism is also a nasty satire of Christianity.
My tastes for these varied works may give something of a false impression though. I'm far from being a rabid atheist, but I am also not easily offended. All I can say is I likes what I likes.