I helped a friend of mine at church (he's the youth pastor) edit together some clips from it for a sermon series. The basic message was a conventional evangelical one, but using analogies from The Matrix was a new twist. I thought he kept the separation well, making sure the borrowed concepts stayed entirely within the movie's framework without trying to find "hidden" meaning in it.
I tend to stay away from those who insist on reading more into it - besides, Evangalion is much more fertile ground for that! So they aren't really trying, are they? :-)
Wade.