I’m with Chuck on this.
The last thing you should do is cringe and censor. By all means read through and discuss the books.
Furthermore, if I were a crafty Hollywood director seeking to gin up maximum publicity for a harmless kid’s adventure movie...
As far as I can tell, in the movie the bad guys are called “The Magisterium.”
Big. Deal. Didn’t our own beloved R.A. Heinlein set at least one of his novels in a period when earth was dominated by an oppressive theocratic state?
At least we know the usual suspects will knee-jerkingly cover it with glory, assuming—sight unseen—it to be christian-kicking.
I understand the "don't give them publicity" argument, but if you think Pullman is not anti-Christianity, you have not done your homework.
As far as I can tell, in the movie the bad guys are called “The Magisterium.”
Also, consider this para from the Wikipedia entry for the book trilogy. Note that The Northern Lights is the original title of The Golden Compass.
In Northern Lights, the story takes place in a world with some similarities to our own; its society seems to resemble the 19th century with Victorian era dress style and steampunk technology level. It could also be speculated that in this world The Reformation never took place; John Calvin is referred to as a Pope. The church (often referred to as the "Magisterium") controls all of the western world and probably the entire planet.
Hope that cleared things up.