You could still let the guys out. Depending on how zealous they've been, the ladies may be thankful to be "stuck" in the run by themselves for a while!
They don't need to be separated all the time, right? Only when you're going to be hatching them, and a few weeks beforehand.
If you only sell one breed (or one at a time) then you could have that breed in a big run, or even just those birds that you are actively breeding, and let the rest out...