If your buddy doesn't want to play D:OS anymore, then there's no point waiting for him, is there? You may as well play, because the current saves will be invalidated once the beta ends and the full game comes out.
I just told you a solution to the problem: If you want to have a start-to-finish co-op experience, keep separate profiles for single-player and co-op. If you want to advance without your buddy, copy the co-op saves and such into the new profile. That way, if your buddy gets time to play again, he has a choice: continue where you two left off, or join your game a few hours later.
The problem you are having is is not a problem with the game, it's a problem with you and your friend.
