Could you fabricate a plexiglass divider and drills some holes in it and seperate them to their own sides of the tank for a while until they get used to each other? It is something I have tried in the past with Cichlids and I had pretty good success with it. The theory being that eventually they will get used to each other and while it may be more headache for you in the shortrun, at least you know that nobody is going to get killed from getting the crap beat out of them.
Another option is to put on of them into a breeding container and float the breeding container in the tank for a few days. Again though this will severly limit the amount of the tank that that one fish will have to roam and may not be the most humane option.
I have read different methods as to which fish should be put in "time out", but it seems like it really comes down to personal preference. If it was me and I decided to use that approach I would put the bully fish in the sin bin, but again I don't think it is going to matter much.
Good luck,
-Ov