Hens have been hatching eggs and raising chicks with the flock for thousands of years. Ancient Egyptians incubated eggs and brooded the chicks themselves long before electricity was controlled. People have been isolating broody hens for a long time. People like to think all this is new or modern but it has all been going on for thousands of years. There is nothing wrong with any of these methods, which way you decide to go is just the way you decide to go.
Yes, bad things can happen if the hen incubates, hatches, and raises the chicks with the flock. Bad things can happen if you isolate her or decided to do any of these yourself. You are dealing with living animals. Good things and bad things can happen. There are no guaranties.
A mature rooster’s instinct is to take care of all members of his flock. This especially includes young chicks. Not all roosters are good roosters but I have never seen a mature rooster harm or threaten to harm a chick at any time. I have seen some roosters (not all but some) help Mama take care of the babies. They are living animals so no one, including me, can give you any guarantees on how they will act but I’ve never had a problem with roosters and baby chicks. Immature cockerels can be more of a problem however.
My hens don’t go out of their way to attack baby chicks but if a chick invades her private personal space she may peck that chick to remind them it is bad chicken etiquette for a chick to bother its betters. Usually that peck is all it takes for the chick to run back to Mama. That’s usually the end of it. If the hen threatens the chick though Mama politely but firmly kicks butt. She does not allow anything to harm or threaten her chicks. You are dealing with individual living animals. Not all broody hens are as good as some others but most are very protective of their chicks.
You can let the hen hatch and raise them with the flock. You can isolate the hen and her chicks if you wish. You can take the chicks away from her and raise them yourself if you wish. She will be upset for a few days but will get over it surprisingly fast. There is nothing wrong with any of this but you might want to isolate her. It sounds like you are stressed, mainly by the unknown. You would probably be les stressed if you isolate her.
Good luck!