We have two coops and have bantams and standards together. We can empathize with the fear of having the smaller hens hurt by the larger ones. At one time, our rooster was aggressive with some of the newer hens so we divided an area of the yard with chicken wire and made some entries into the fence along the bottom. When the smaller hens wanted to get away from the rooster, they would duck in through the opening and the rooster could not follow. After about 4 weeks, everyone got use to one another and we took down the fence. We use this whenever we want to introduce new chickens into the flock.
Our yard is quite large so we drive wooden stacks into the ground and staple the chicken wire to the stakes, then cut out openings - we show the chickens where the openings are and put some scratch in there - they get it pretty quickly.
Good luck!