The writer of the story seems to be arguing that having an extremly controlling government is evil. The book is more geared toward the magisterium representing a church instead of a government, the movie does not make it clear exactly what the magisterium represents.
Philip Pullman says that his book does not attack Christianity nor does it promote atheism. "My point is that religion is at its best — it does most good — when it is farthest away from political power, and that when it gets hold of the power to (for example) send armies to war or to condemn people to death, or to rule every aspect of our lives, it rapidly goes bad. " He simply wanted to show that power corrupts even the best, "I think the qualities that the books celebrate are those such as kindness, love, courage and courtesy too... And the qualities that the books attack are cold-heartedness, tyranny, close-mindedness, cruelty," says Pullman.
There is no reference to God at all in the movie nor are they tring to over throw a God, the movie is simply a story.