It's actually fairly normal for a bossy hen that Is used to not having a rooster to have a bit of a scuffle in the beginning. He has to win them over, and show his dominance. I had a hen who never accepted a cockerel(7 months old, basically full grown) and every time he would try to become flock leader she would kick his butt. Hr probably would've eventually won but I was tired of them sparring so I replaced him with a grown rooster that she accepted immediately. Do his attacks seem viscous or more like he needs to shoe her who's boss? Social structure amongst chickens isn't always pretty to us, but is necessary for them. I've never seen a decent rooster attack a hen... I dont believe a sane rooster sees a possible mating opportunity as an intrusion, another male yes, but a female, I doubt it. I would vet that one of two things is happening: 1. She is older/larger than him, and therefore not going to submit. This would be a good reason to separate, because he will keep trying and could easily lead to bloody combs etc.. Or 2. Hr is an immature cockerel or not a good mentally sound rooster and is actually just attacking her.
How are the interactions between that hen and the rest of your girls?
What are the ages of your girls & rooster?