The handling of Christianity in the film...
...was done fairly well, I think. None of the early Christians ever come across as unlikable. Jacopus in particular. He never belittles the villagers for their beliefs and seems very kindly and grandfatherly.
Even the one time he comes close to insulting them ("You call yourselves Christians?") it's more shouted in desperation and fear than anything. He probably honestly believed that if they'd remained with him, they could've defeated the dragon. And while some may consider him stupid for standing up to Vermithrax all by himself, I see it as being a sort of "foolish bravery" if you will. Stupid yet admirable all the same somehow, sort of like Elspeth later.
And while the newly converted villagers do claim that the dragon's death is God's will, they don't rub it in. This outcome of things is treated as being an inevitable "passing of the torch" in terms of belief systems. The new comes and replaces the old, just as Galen himself takes up Uhlrich's mantle (and to a lesser extent, Greil replacing Jacopus). The story doesn't judge this passing, merely presents it and lets the viewer come to a decision.
The character of Greil is also interesting. You'd think that witnessing Jacopus' death would convince him that the priest's God is false, or at least offers no assistance against evil. And yet it's clear he is deeply affected by seeing Jacopus die after taking such a brave stand against the dragon, and the reason he converted was likely due to seeing the inner strength and resilience that belief in Christianity gave the doomed priest, even if it was of no practical use in that particular situation - i.e., if it could give Jacopus so much inner fire that he could stand his ground against a dragon, then it (to him) must be worthwhile.
"I mean, really, how many times will you look under Jabba's manboobs?"