I should also have mentioned James Blish's A Case Of Conscience:
Ruiz-Sanchez’s scientific discoveries on Lithia seem to him to contradict Catholicism. If the Lithians are apparently good without divine help, then they are really created by Satan to mislead mankind even though Catholics deny that Satan can create. Pope Hadrian VIII helps Ruiz to resolve this conflict by regarding the Lithians as a demonically-induced hallucination but how plausible is that? If Satan does not, we think, induce planet-wide hallucinations on Earth, why should he be able to do so fifty light years away? But, in any case, mere contradiction of Catholicism would not make the desire for secular knowledge evil.An atheist defeats Ruiz by influencing UN policy on Lithia. A lapsed Catholic inspires awe in Ruiz by communicating instantaneously with Lithia. Thus, secular scientists dominate Ruiz’s period for both good and evil, communication and destruction.
-copied from here.
Poul Anderson's Cainites are superficially similar to Blish's Lithians in that neither species has any concept of God. However, the Cainites lack the moral goodness which troubled Blish's Jesuit character when coupled with complete ignorance of God. Nevertheless, Anderson, in this and other works, addresses the same theological issues as CS Lewis and James Blish.