Are you sure the flogging is not just him doing what roosters do? A good point made was perhaps the head hen is being difficult. He may not be the only one at fault here.
Good Point!!
When I first started with chickens I had previously had a bad experience with a mean rooster so I decided I didn't want one.. For two years I had hens, One of the hens, a BA was top flock master, even mounting some of the hens... When we decided to increase our flock and got a rooster she not only would not allow him to mate her but would fight him off the other hens. It took him about 2 months for her to finally submit and had I known about all this then I may have very well gotten rid of her as she was obviously the problem..
I've not tried this myself, but have seen it recommended many times on BYC here...
When the lead hen is causing problems, quarantine her for a few days to a week. When you put her back in the flock she will be at the bottom of the pecking order.
I'm sure there are nuances to this method and it may not work with all birds, but might be worth a try if you still want to try to keep your rooster. (I'm speaking to the OP).