I'll preface my post with this: I am an atheist. I am not even a "spiritual" atheist, as friend White is. Largely, I simply don't understand the concept of religion, beyond that it offers hope. The trappings included, as well as the certain moral dogmas involved are really beyond my comprehension. However, I believe that people will follow a religion that closely matches their moral compass, rather than following a religion first, without forming a moral compass of their own. In this, I can see why someone would choose a specific religion over another, but not as to why to worship in the first place.
I mention these things not to spur a religious debate - they often turn ugly, and while I may not understand why you follow your beliefs, I certainly respect them, and don't wish to demean the discussion by arguing over who is right about the existence of a Supreme Being. I was raised religious, so I doubt I will be converted by any arguments made, and by the same token, I doubt anything I say would cause you to turn to an atheistic viewpoint. - but rather to let you understand where my perspective comes from.
Now, for the issue at hand, I certainly believe that parents should be informed about the content of what their children might watch. It is a parent's right to raise their children as they see fit - regardless of whether or not others agree with their parenting decisions (Within reason, of course. Abuse, etc, is obviously not something that falls under the discretion of parenthood).
However, I disagree highly with calls to remove the books from library shelves, etc. With libraries in specific - I am a tax paying member of society, and as such it is a resource available to myself, as well as practicing members of various religions. As an atheist, I do not feel books containing quasi-atheistic ideals (And I would argue that the "theology" that Pullman portrays is a hyperbolic caricature of real atheism) are fit to be removed. If I had children, I would not feel that that would be a sufficient reason for them to have a chance to pick up the books and read them while browsing. Municipal libraries are a government entity, and as such, should not exclude content because of religious context. The separation of church and state exists for many reasons (Including protecting the Church from the Government, which has shown itself to not exactly be a stable and well performing force over the past decade!), and is quite applicable when dealing with a government funded library.
Part of it is a personal opinion, as well. I believe that most children who will read books for entertainment are the more intelligent of the crop, and are likely able to make informed decisions for themselves long before we believe them to be capable of doing so. I do not believe that any child secure in their faith is going to be converting to atheism after reading a fantasy novel. If reading a story, even a well written one, is enough to cause the conversion, than undoubtedly other factors could easily sway them as well, ones that they are likely exposed to on a daily basis. I myself turned from Christianity to Atheism during junior high, while attending a humanities class. The teacher was very devout, and never pushed any students towards atheism, but our studies were heavily focused on religion, both today and in ancient culture. I came to a personal conclusion that, fundamentally, Christianity is no different than the worship of Ra, Zeus, or Quetzacolt. This conclusion was not the result of the teacher pushing us in that direction, or some novel espousing atheism. It was made based on opinions I had formed from many sources over several years. I would highly suggest that we give more credit to the children that would be reading these books in the first place - I would argue that they are not going to change faith based on a fantasy novel.
I also disagree with the call to remove it from book store shelves. By all means, call for a boycott of the book, refuse to buy it, etc - but also be courteous and realize that other people who do now follow the same belief system as you could want to buy the book, and having it removed is an inconvenience to said people. At the age where you would be censoring your child's input, you should be there to buy their books with them. You should know what they're reading, and understand what is in it. Calling for a blanket ban on the book, in my opinion, is shirking your responsibility as a parent, removing yourself from a personal inconvenience directly dealing to raising your child, and then forcing it upon everyone else. We are uninvolved in what beliefs you would like to teach your child, and whatever censoring you would like to place upon the material they read, and as such, it should not become a matter where we have to deal with these issues. If you do not believe that your child should read these books, then it is a matter that you should enforce, rather than trying to have it enforced on everyone.
Ultimately, I just feel that trying to have the book removed from libraries and stores is an extremist reaction to something, and that instead it should be a personal decision: Do you let your child read the books/watch the movie? If not, that is your own prerogative.