I sort of figured as much. But that's assuming they ever get to make "The Subtle Knife." They may have lost their chance.
It would also create an imbalance in the dramatic structure, for the over-the-top nature of "The Golden Compass" book's climactic scenes, as well as the shocking twist they contain, makes them work far better as the ending to a film than they would as the opening to a film.
I could, however see the filmakers ending a film of "The Subtle Knife" somewhere in the early chapters of "The Amber Spyglass." TSK is the shortest of the books, while TAS is, by far, the longest. And TSK does not have as awe-inspiring a climax as "The Golden Compass."