(For who have yet to read The Subtle Knife, this post may contain some spoilers. None are essential to the stories of Lyra or Will or the choices they make, but I felt you might want to be warned at the very least.)
I finished His Dark Materials a few years ago, and thoroughly enjoyed the books. I never hopped onto the Harry Potter wagon, nor any other recent children's series, but HDM intrigued me before I even understood the scope of the story (in fact, I may have been sold based on this fan drawing of Iorek). I enjoyed them so much that I bought an audio copy of the third book to entertain me on trips between my hometown and the university, and while listening to it recently, it occurred to me that Christians are missing out on an opportunity to use HDM for Christian ends but that this might actually be to their benefit.
For those who aren't familiar with the trilogy, the the major story arc is concerned with the development of sentience, the acquisition of the knowledge of good an evil, and the relation of the two to sin. Like Adam and Eve, the children's quest takes them to a point where they are tempted on a matter somewhat unrelated to the major objectives of the adults in the story (who are the one's out to kill The Authority, not Lyra, despite what some are claiming). The backstory and the explanation for much of the more magical elements concerns the development of consciousness in matter. The angel-like beings in the books were simply the first to develop consciousness, and The Authority, the very first, lied and said he'd created all of the world.
The books leave one question wide open: how and why did consciousness arise? The books give a partial answer, but it is still unsatisfactory for the elements involved need not have been there. In the eyes of ID proponents, the very existence of matter and consciousness in the stories demand a world-internal creator. The entire story could be read as false-prophet Authority facing his punishment for assuming a role not his own while the real watchmaker sits in the background watching his world tick. The books can (and perhaps should) be read as a warning to liars and those who presume to know more than they do or take a power that is not theirs. The books do not deny that reading.
Yet the reason why ID can be invoked to explain life and consciousness in HDM is exactly the reason it is rejected by scientists: ID makes no predictions. It could explain a world with half-human half-vulture harpies and simple devices that always tell the truth as well as it could explain our current world. That HDM is specifically intended to be a world where there is no creator but ID can still purport to explain that world is an example of ID's failure to explain anything. If it can be applied to the godless world of the book, how can we be sure that our world is not godless and the arguments IDists present are not just false positives?
To invoke ID (or the argument from infinite regress or any other popular theistic argument) in the world of HDM is to demonstrate their vacuousness.