Yeah, I don't think it's anti-God either. Zachy, I think the quote you're talking about is where Pullman says that the book is about "killing God". But, in the stories God has a fictionalised origin where he was the first angel to exist and he convinced other angels that he made them. In the stories, God and the Authority are corrupt institutions that seek to essentially enslave a population of people by removing their souls in order to make them docile.
If anything, the book is anti-authoritarian, not anti-God. Although Pullman is an Atheist, he says something that I found to be wise:
Quote:
The religious impulse – which includes the sense of awe and mystery we feel when we look at the universe, the urge to find a meaning and a purpose in our lives, our sense of moral kinship with other human beings – is part of being human, and I value it. I'd be a **** fool not to.
He does accept that religion isn't just a destructive force that is vile in every way. He's against the history of violence that has been done in the name of religion (though I argue that power and property were the real reasons for these actions).
The books are great and if you're firm in what you believe, it shouldn't bother you in the slightest to read a book that suggests a different view.