I've never had a dominant rooster threaten a chick. I understand anything can happen with living animals but his instinct should be to protect those chicks or at least not harm them because his instincts should lead him to consider them his offspring, even if they look totally different. I...
Personally I let my broody hens incubate, hatch , and raise chicks with the flock. As you can easily see on here, many people do all these differently. If you decide to let her incubate, hatch, or raise with the flock let me know a bit about your situation and I may have some suggestions...