We had this problem but with all hens. They mostly liked him, but he would sneak up while their backs were turned, and as far as I was concerned, raped them. They were just jumped and bred, they were young, and screamed bloody murder. PLEASE no one admonishing me for using the "rape" word concerning my chickens. I've already been informed that word does not apply to chickens. But we still at this moment have freedom of speech. Thank you.
So, while the pullets got more used to being raped, because he hit the less dominant ones over and over, they became totally denuded on the back, reminding us of a Perdue chicken in the store.
After he started protecting the girls from me, even when I was feeding, watering, cleaning, and ignoring the flock, my husband was forced to build a mini chicken coop and another smaller run. He has access socially, thru the fence they all visit and talk to him, and he can see entire chicken yard so he does watch everything. He will not sleep in his coop, but on top of it.
Without a husband, I'm pretty confident I could built a water proof shelter, ladder, and chicken run. It would not be pretty, but it would be done.
After he moved, my second lead hen started the same thing. Surprise and forced over breeding to the point the feathers stayed damaged. She is female, but there it is. She moved in with the Rooster, and is bred maybe once a day instead of every fifteen minutes, which is his preference. There is an argument before each breeding. But it doesn't progress to serious or injuries. I would think with your lead hen and Cockerel, the argument maybe got nasty and she lost, had a little injury, and he traumatized her. I would treat her like she has PTSD, which of course that level of stress and anxiety can cause a whole snowball of problems in the flock.
Maybe she's your be first house chicken? Just joking, but however you figure it out, they need to be separated for now. I'm sure when she "gets" that you stopped his access, she will feel much better?