Here's what Mr. Pullman himself has to say on the matter (he echoed similar themes in a talk that I saw a few weeks back):
I've always made it clear that theocracy - the political exercise of religious authority, which is what the Magisterium in the story embodies - is a special example of the regrettable tendency of humankind to believe in "one size fits all" answers: to cling to the extreme of dogmatic fundamentalism whether religious or not. In fact (and I've pointed this out too many times to go through it all again) the purest example of theocracy in the twentieth century was Soviet Russia. So I have no problem with the way the film has put the emphasis; it could hardly have done otherwise.
Then he drops this bombshell, when asked why the "His Dark Materials" books do such an elaborate examination of Christianity but neglect to mention Mr. J.C. himself:
His omission from HDM was deliberate; I'm going to get around to Jesus in the next book. I have plenty to say about him.
Whoa Nelly! Could this be the long-awaited Book of Dust he's referring to?
And to all the people whose eyes glaze over with all this talk of religion, I have one thing to say to you. Go see the movie if only because it has a kick-ass armored polar bear voiced by Ian McEwan. (He's not smiling)