You hear so many bad things about roosters being dangerous to the flock on here and practically all of it is just crap. Chicks have been raised by broody hens with the flock since there were chickens. If they are exposed to the chicks at an early age practically any dominant rooster will think they are his offspring even if they are a totally different color and look nothing like him. Some dominant roosters help Mama take care of the babies, some don’t, but most dominant roosters will protect their entire flock, babies and all. I’ve never seen a dominant rooster even threaten a chick, let alone do harm.
Non-dominant roosters can be a bit less helpful but if they are mature they are not likely to threaten the chicks. Cockerels, males that are not yet mature, can be more of a risk but Mama usually has no problem teaching them to leave her babies alone.
I think a lot of people confuse an immature adolescent cockerel with a mature flock master. There is no comparison, they are totally different things in behavior. Even with a lot of cockerels being raised with the flock I’ve never had a problem with them harming the chicks. Mama takes care of that.
You do not need to separate the rooster. You need to leave the rooster with the flock so he can take care of all his flock.