When I mentioned this in discussion forums, several people said that that was just my Christian prejudice. So I was interested to find a review from someone more sympathetic to Pullman's worldview saying the same thing. Reason Magazine - A Secular Fantasy
While Pullman has said that he is interested in “telling a story, not preaching a sermon,” he slides more and more frequently into preaching as the story goes on. Some of his favorite ideas—for instance, that the human body with its senses is far superior to the fleshless spirit of the angels, or that the best afterlife is to become one with nature—are stated again and again and again and again. The idea that the transition from childhood innocence to adult experience should be welcomed, not feared, is illustrated by a heavy-handed plot twist in which Lyra and Will’s sexual awakening proves to be the key to the world’s salvation. When ideology and literature collide, literature suffers. The Amber Spyglass is not quite on a par with the first two novels: Its new characters and worlds are generally less interesting, far too much space is given to sententious musings about the meaning of life in a post-God world, and eventually you start to feel that Pullman is trying to cram too many messages into his narrative, even if that means unnecessarily dragging it out.
I recently reread the books, after seeing the film The Golden Compass, which is based on the first book of the trilogy, Northern Lights. I enjoyed it more on the second reading, but the preachiness was still there. So too was what seemed to me the biggest weakness in the whole plot -- that Pullman, after making clear that he rejects the ideas of Christian asceticism, has his protagonists end up adopting something very similar. They end up like Abelard and Heloise, or Leon Bloy and his love.
On the notion that adult experience should be welcomed, not feared, however, it seems to me that Pullman's message is ambiguous. I recently read Lisa Chaney's biography of J.M. Barrie, the author of Peter Pan. Barrie had a horror of children growing up, yet recognised that Peter Pan was somehow inhuman, because he was deprived of so much of human experience. But in His dark materials there is something similar. Pullman's protagonists go on to live rather dull adult lives, forever separated from each other, and can look back on their childhood as a time of joy, excitement, adventure and love. Growing up doesn't seem to have all that much going for it.