What I got from the RPGcodex article was that you'd control your companions most of the time, but at certain key moments, the AI might take over. Like, if you watched one of the videos, Hudson is an assassin, and he can team up with these other assassins that attack the rest of the companions on sight. So like, maybe if you wandered in there as a whole group, he might actually side with the assassins and try and kill the rest of your party :P
Sounds ridiculously hard to make work well, though. Swen has been justifying the focus on multiplayer by saying that making all these different routes and activities available to multiple players will also strongly enhance the roleplaying experience for one player, which I think is true. I'm really not worried at all that the single player experience will suffer, and I might actually play it multiplayer.