I think it depends on what you mean by fight it out.... certainly you don't want any damage done, so if they are staring each other down and hopping on each other, etc. that is one thing - but if they are really going at it and fighting lots then they should be apart. Are they fighting over hens? Maybe you need more hens? They have to battle it out with one alpha winner... If the omega does not want to give the title to the alpha and is putting up a fight, then either get more hens and give them more space (or separate space) or they need to be completely apart.
I just rehomed our alpha roo, but before that our two got along fairly well -they each accepted their place in the flock.