I think the best solution I've heard was allowing us to teleport npcs to a far-flung corner of the map. They could make it so you can't teleport them until any objective they are tied to is complete, that way they would appear to disappear, but nothing gets broken.
I doubt the coding issue is that dramatic. some Cryptic missions have NPCs that change allegiance when you talk to them. this suggests to me that the base code is in place and functional.