Consider this interpretation. The radio said that people were being taken away by the aliens, and at several points people wonder if it's the end of the world. Well, what if it actually is? In the Christian biblical book of Revelation, all of those who are saved are taken up to heaven, and all the sinners are condemned to hell.
Now, since the story is obviously trying to point out that having faith is a good thing, I think we need to turn this on its head a little bit, and say that the aliens are, in a way, a representation of some sort of hellish agent, that takes all of the sinful to Hell. . . . Or space, or whatever.
Of course, I know this seems a little far fetched, but consider that the method of defeating them is discovered in the Holy Land, where, you'd think, most people are faithful to their God, this begins to suggest that the aliens could not harm those who are faithful. Then, of course, there's the fact that water harms them, just as holy water can supposedly drive off fiends and demons (and hey, the water at the end was all inside the house of a reverend, so maybe it was blessed; *grin*)
The kicker that makes me give this theory credence is that the last alien comes back for Graham Hess after all his fellows have gone, because Graham still has to decide his faith. If he ignores the signs, and is faithless, then the alien would have killed him. The alien actually just seems to wait for Graham to make up his mind.
Add in some symbolism that the son (seemingly) dies and then comes back to life, an act which reaffirms Graham's faith, and I think it makes a pretty good theory.