The issue is that many (most?) Sci-fi nerds, myself included, are irreligious and find it a bit strange when the two mix.

That isn't necessarily a problem on its own because a character can be religious and still be a great character (obviously).

But when the plot kind of pulls that sci-fi rug away from underneath your feet and goes "boom, Jesus" (voice of Peter Griffin from Family Guy), it feels a little awkward.

It would, imo, have been better if the movie ended on some lingering question about our place and meaning in the universe, like Morgan Freeman's epilogue in War of the Worlds.

I mean, not necessarily. Humans are smart enough to travel to the moon and dumb enough to give ourselves cancer and pollute our own planet.

I mean, our air is filled with water molecules, so they'd die as soon as they landed, anywhere, if we use logic. :)

Yes, I agree. This is often the case with these types of films, sadly. The ending usually disappoints either simply because the mystery is gone, or because the resolution is executed poorly.