I believe religion will always be discussed in science fiction. There's just something about it that will always be of interest, whether you're religious or not.
The "big three" of science fiction, Arthur C. Clarke, Asaac Asimov and Robert Heinlein, all nonreligious, wrote great stories that involved religious themes (most notably "The Star," "The Last Question," and Stranger in a Strange Land, respectively).
There also are many authors who have written great stories with religious symbolism. I personally like the Space Trilogy by C.S. Lewis (although he's known more for his fantasy) and the Firebird Trilogy by Kathy Tyers. The Book of the New Sun by Gene Wolfe is another story known for its religious symbolism.
If you want to read the short stories "The Star" by Clarke and "The Last Question" by Asimov, the following websites have the full text of the stories:
Let me know if there are any other good religious-themed stories you'd like to point out.