So? Find a way to make it work. If the players really want it to happen, then they have to work together to make it happen. One side doesn't get to sit back and say "Well, we'd really like to not wipe you out, by it's my character. You know, I can't really control him, and he wants to wipe you out, so... tough luck."
If you want to save Melhed, then find a way. Will it come back to bite you later? Maybe. But then you have a built in enemy, the next time you need one. And, really, it's a game. Who cares? If you don't like the way it's going, then change it.