Can't agree about the verdict on either Case of Conscience or Stranger in a Strange Land given above, as I'd say both (especially the Blish) are much more finely nuanced than that. Blish, for example, walks a fine line on whether the view the priest takes is valid or not, or whether the outcome is brought about by purely physical means and human greed; while Heinlein's exploration of faith and various religions (not always the same thing) has many levels to it, as well (not to mention a fair degree of humor).
There have been quite a few sf books to deal with the subject in various forms. Some of those I've found of particular interest are:
A Mirror for Observers, by Edgar Pangborn (a sf retelling of the Book of Job; quite poignant and an examination of the themes in the biblical account as well)
The Day the Sun Stood Still -- three novellas, by Poul Anderson, Gordon R. Dickson, and Robert Silverberg, with an intro. by Lester del Rey
An Exaltation of Stars -- ed. by Terry Carr; while not restricted to religion, the tales here are definitely concerned with explorations of it
Deathbird Stories, by Harlan Ellison -- an examination of modern "gods" and religious/mythical tropes and ideas
A Canticle for Leibowitz, by Walter M. Miller, Jr. -- possibly the single greatest sf book on the subject, and simply a marvelous book which is alternately humorous, tragic, troubling, and uplifting, and always thought-provoking.
Behold the Man, by Michael Moorcock -- a time-traveller who goes back to the Holy Land to find out the truth about Christ, and ends up with more than he bargained for... or was this really the reason for his going?
These are only a few; there have been many, many others, both novels and shorter tales, no few of which are very good and excellent for provoking questions (Clarke's "The Star", or Silverberg's "Good News from the Vatican" being among them....)
EDIT: Though there are problems with this particular list, you may find it at least helpful and suggestive for further research:
http://en.wikipedia.org/wiki/List_of_religious_ideas_in_science_fiction