Golden Compass was not successful. It bombed in the theatres and no sequel is planned. They also did entire portions of the story completely out of sequence.
I found the characterizations in the book itself to be less than interesting. I had hoped to read the following books but was really quite disappointed by the end of the first one.
HOWEVER. There is nothing controversial at all until the third book, really, and in the movie, you wouldn't know the Magisterium was the church unless you, well, already knew that in the first place.
And if that was more than you were looking for in an answer, then my mission is complete XD
Right after I got done with Harry Potter.
And I freakin' loved those books...
Of course, I'm so dense I tend to miss stuff about eighty per-cent of the time