I can stomach the various references to God throughout the movie. That's just dialogue. I had no problems with Anna being religious, either. Some people believe in God, others don't. Heck I could even stomach lines like 'turn to the light' and 'God didn't do this, Anna; we did', which, by themselves, don't say anything too overt about religion. But when these things are taken along with some of the other things... In one of the final scenes, for example, Smith, a man who has survived by nothing more than God's good grace, stands face to face with the leader of the creatures, the very embodiment of perverse science. He keeps screaming 'I can save you!' and the guy just keeps literally banging his head against the wall. I'm not remotely cynical, and even I just sat there rolling my eyes. Yeah, like it's not obvious what
that's meant to represent.

;
The next scene was even worse. The two survivors open the door of the safe zone to find...a church. With little kids scampering happily away from it. Seriously? That's like making a film where racism is a central theme and saying at the end 'black and white people are different, and sometimes that causes problems'. Religion can be an interesting theme to tackle, but if you can't convey your view tastefully, don't convey it at all, please.

Leave a good movie as a good movie, and leave underlying themes to those who know how to handle them.