I just finished a great game called "Dead Space" in which religious nutbars try to destroy the human population with their idiotic drivel and the government eventually steps in and does something, but only after thousands have died as a result of their delusion.
I also am a fan of Fallout 3, in which religious people are represented largely as harmful by their stupidity, gullibility, and manipulativeness, albeit with a few minor exceptions.
Half life 2 seemed a bit religious, as the ancient faith of the weird aliens seems to be powerful, but then it seems to be ultimately controlled by that weird guy that appears every so often.
Bioshock? I dont really know if that is or not...Id be interested in opinions. What about other games?