I'd have to see the chickens and matings before I'd make a decision on whether it is causing any harm or not. Are you seeing any blood or injuries or are loose feathers just flying off? To me it is a lot like integration, if no injury is being caused no injury is being caused. Flock relationships can be pretty complicated. Chickens mating is not just about a sex crazed maniac raping the hens, a lot about it is about dominance and other social interactions that help a flock function.
When some chickens molt you can barely tell, mainly just by some feathers flying around. These are the slow molters. Some don't even look that ragged. A fast molter may drop feathers by the clump, having a lot of bare space. There is some more risk to the hen from the rooster's claws and spurs if the skin is bare, especially if the hen is resisting. These are the hens I'd watch to see if there is any real damage. I've never separated a rooster when they are molting and never had a molting hen damaged. I tend to let my chickens be chickens.
Should you separate the baby chicks from the flock? Some people do for their own reasons. Based on their experiences they may have some good reasons. Some of that might depend on the personalities of their individual chickens or maybe their specific set-up. That may be space or even the kind of coop they have. Everyone can't do things the way I do it because we are all unique. What works for me does not work for them.
I don't separate my broody-raised chicks from the flock. Sometimes my main coop is really crowded so I lock a hen and her chicks in a shelter in my run for a couple of days and nights so the hen will take them back to that shelter so I can lock them up at night safe from predators, but after a couple of nights I open it up and let them roam with the flock during the day. If the main coop is not too crowded I just let the hen manage them.
I've never had a broody hen that would not protect her chicks from other flock members, some people on here say they have and I believe them. When you are dealing with living animals about anything can possibly happen. I've never lost a chick to another adult flock member. I had a two week old chick kill its sibling while the broody watched. That could happen if they were isolated. I had a baby chick get into a pen of 8 week old chicks where Mama could not protect it and they killed it. To me that is one of the biggest risks in trying to isolate a broody and her chicks, the chicks may get somewhere Mama can't protect them and they are in danger.
To me a big advantage in letting a broody raise her chicks with the flock is that she handles integration. From the time they hatch until she weans them she is teaching the other chickens to leave her babies alone and letting them get used to having the chicks around. I've had broody hens wean their chicks and leave them on their own to make their way with the flock as young as three weeks, I've had some go for over two months before they weaned them.
These weaned chicks have to handle their own pecking order issues that determine their rank in the flock. That won't happen until they mature. With my pullets that is usually about the time they start to lay, with cockerels it can be all over the board. Until they mature and force their way into the pecking order (usually a really peaceful process for the pullets) the chicks will rank below any more mature bird. The chicks handle that by avoiding the older birds. That's where space comes in to play. If they don't have enough room to avoid the older birds they can be in real danger. If your space is tight I'd be more worried about the chicks after Mama weans them and quits protecting them. If your space is that tight you are probably going to have issues trying to integrate them laer if you isolate the hen and chicks anyway.
Another reason I'd want the rooster around. I've never had a dominant mature rooster threaten a chick with a broody hen. I have seen a dominant mature rooster help Mama take care of her chicks. I have seen a dominant mature rooster protect all flock members, including a few after they were weaned. Not all roosters do this. Some just ignore the chicks. Some members of this forum have said they have had roosters attack and kill baby chicks. You don't get any guarantees on how any living animal will behave, but I've often found it be beneficial to have a mature rooster in the flock when Mama is raising babies.
I don't know how much room you have. If you have them shoehorned into a small space the odds of behavior problems are much greater now and later than if they have a lot of room.
Good luck! This can be a fun experience, watching Mama take care of her chicks. It can also be nerve-wracking, especially your first time and before you have seen a broody hen at work.
Generally roosters tend to leave molting hens alone. If he is breeding them and injuring them, I would separate him from the flock until the molt is over. Many folks successfully raise chicks protected by broody hens in the flock population.
