It's not an inappropriate question at all--we like this kind of stuff around here.
My thoughts on Pullman are actually the same as my thoughts on Lewis: as long as it's good writing (and Pullman is a stellar writer), I don't care what his views are on religion. I read all of the Narnia books when I was kid, and had no idea they were supposed to be Christian. I pity anyone who likes them because they're Christian, rather than because they're good, because that to me is a completely wrong-headed way to approach art. I love Roger Ebert's quote on the subject: "It doesn't matter what art is about, but how it is about it."
Ironically, while I actually enjoy Pullman's word-for-word writing much more than Lewis's, I think Lewis is able to carry out his allegory a little better. By the end of Amber Spyglass (the third book in the series), Pullman has pretty much dropped all pretense of allegory and has his characters start spouting off unsupported love letters to atheism. Please note that I'm not complaining about the atheism: his depiction of God as an ancient, broken being was really cool. I can read about that in a fantasy book and not feel threatened by it religiously. What I am complaining about is that the messages started to get way too heavy-handed by the end. The quality of the writing and presentation fell apart, and that disappointed me.
As for whether the movie will be overtly anti-Christian, I don't know. I highly doubt it. Most of the Christianity in the first Narnia movie was completely drained out, and I imagine The Golden Compass will be the same (although honestly, there's not a whole lot of anti-Christian stuff in that book to begin with).