The Golden Compass Controversy??? Please Answer!!?

Okay, so I recently read the 'His Dark Materials' Trilogy -- they're amazing -- and I see why so many people were boycotting the movie now.
We're writing a free-topic paper in english now, and I would really like to do mine about this controversy, but I'm running out of specifics.
I know the basic stuff:
Magisterium is supposedly catholic Church, they kill god in the end, taking away their free will, etc.
But can anybody give me some more specific examples of anti-christian pro-athiest stuff??
Okay, settle down.
Just to make this clear to you all, I am not religious whatsoever. I would not call myself an athiest yet, but I am not taking sides with this question at all!!!!
It's an english paper, and it is not opinionated. I'm just asking for specific examples from the book/movie to use in the paper.
 
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