It might not be that hard to separate it. Updating the engine to be somewhat compatible with 3.5e and utilizing the OGL is really all that would have to be done. According to the Open Gaming License, the system for 3.5 can be used (which is why you have so many retro-clones, Pathfinder RPG, Knights of the Chalice, Chaos Chronicles, etc), but none of the copyrighted materials (that would be NPCs, worlds, specific monsters like the Beholder, etc).
Or, if one had the source code, putting a different system around the engine could be done (or if it was going to be rebuilt from scratch). So, not totally impossible. But, whether or not it would be worth it would be another story.