What I suggest is a co-op mode that would have the second player temporarily control the first player's previously recruited companion... (it could simply be an option on the companion wheel). That way, there would be no lore problems, and the balance of enemies and obstacles wouldn't need any adjustments, because even without co-op, the player would still have help from the companion.
If you hate this idea, no need to flame- this is just for the sake of discussion, I'm not trying to insist on it. What are your thoughts on this idea? Would you be cool with it? If not, what's wrong with it? Can anyone think of a better way to integrate Co-op?