it's not very often I encounter such perception and good instincts. You have them. Trust them.
Humans have preconceived ideas as to how things should be. Hens in a flock happily submitting to the rooster is one of them. That's not how things work in real life. In real life, higher life forms have "agency", meaning they make decisions to optimize their survival. Their individual perceptions guide them. Chickens do this.
If we try to force our "rules" onto our chickens and ignore their decisions as to what is best for their survival, we can cause problems or aggravate problems that might otherwise be resolved by our chickens. Some hens simply do not like the rooster and they become very stressed when forced to submit to a rooster that they feel does not respect them. Not all roosters have the hens' best interests in mind. Some are real jerks.
And occasionally, a rooster can turn into a psychopath and do real harm to a hen who rejects his advances. I had this happen in my flock. Even though I had been aware that this one hen absolutely refused to allow one of my roosters to mate her and I had her in her own run, one day I wasn't paying attention and tragedy struck.
She was out free ranging at the same time I let this rooster out. He wouldn't take "no" as an answer when he attempted to mate her, and instead followed her into her run and then pursued her into her coop where he cornered her. In the struggle, her resisting and him trying to get her under control, he scalped her, and I mean her scalp was entirely flayed from her head. The blood splatter made for a very gory scene, indication the hen had been severely injured.
After than, I kept her penned, rarely letting her out. In spite of that, this rooster would attack her through the fencing, working himself into such a rage that he ignored the 10,000 volt shocks her was subjecting himself to as he was throwing himself at the fence.
Why didn't get rid of this guy? Because he was a perfect gentleman with all the other hens, and this hen didn't live much longer after this incident occurred, as she was getting on in years.
I urge you to listen to your instincts and try to accommodate your hen's desire not to be assaulted by this rooster. Don't risk a tragedy as I had.