Yes, putting them in a separate set up might work... it might not, but it is more apt to work than how you have it set up now. Roosters are a crap shoot, and rather unpredictable. The above poster that got it to work has a very large run, more space generally, kind of, sort of, most of the time...
You are hoping for a bye, maybe you got one, probably you didn't. The more roosters you have, the greater the chance of things going poorly.
Most inexperienced people vastly underestimate the violence of a rooster aggression, either to themselves, to the hens or to other roosters. It can be...