Batman has been involved in situations in which people had their psyches forcibly altered for the supposed greater good and posted no protest. He has even done it himself in King's run with Psycho Pirate's mask, though this is obviously after Identity Crisis rather than before so I suppose it wasn't precedent at the time. Mentally altering someone hasn't even been something I've seen him struggle or deliberate on outside of Identity Crisis.
You can't really use the idea that he's against someone because if he was for it he could deal with his villains permanently as an idea. That opens up a can of worms and the actual answer is "gotta reuse villains."