I admit, I wasn't there for that part of the scene, so I don't know how it came off, but Christianity was never intended to come off as a boogeyman (that would have irked me too - it's so cliched.) However, the god of the culture Anders stumbled across was so pissed at Christians (with some reason, but still,) that he would attack anything associated with Christianity. In-character, he's just a bit biased, ya know? The only Christians actually mentioned in character sheets or game materials were the monks who raised Anders, who were pretty good people. The religion just wasn't a good match for him.