I agree with the idea of putting wire mesh in the coop, and segregating the chickens in that way. That is what I have just done, and it is working out fine. I have a hodge podge of different kinds of chickens, so it's interesting to see how the pecking order is working out. But now I'm trying to do that idea in reverse with my roosters. It's not working for them though! They want to be with their girls, and keep getting back in the main coop!
Good luck!
Good luck!