You may have a "real world" logic problem there, but game wise it's not a problem at all. You just ask the player if he's willing to be teleported (unconscious or not), or simply decides if he's willing if it's an NPC. It's a world of magic, after all, so it's not really a problem if your "soul" decides if you're a willing target, unconscious or not. Or you could say that he's "incapable of resistance", and would be teleported anyway, if you prefer (I've not really decided what I prefer myself, yet).