Dude, that's nonsense

. If anything the story portrays christians in a rather nasty way, seeing how the templars/chantry generally come off as idiots. Take the endless conversations of Morrigan vs Alistair for instance, wherein Morrigan is clearly intellectually superior and Alistair just comes off as a dumbfuck. Or the crazy sect guarding the ashes of Andraste high up on the mountains. They obviously represent the crazy sectarian cultist evil-fundamentalist stereotype. Contrast this with Stens strong qunari ethics (reminescent of both 'pagan' indian spirituality and kantianism) or Wynne's humanism. They clearly come off better.

If anything, you could remark Bioware took a rather harsh stance on medieval church practices, disregarding the psychologically beneficial effects religion can have.