My rooster is wonderful. I've always handled him and still do. He does get protective of the girls, but that's his job.
He covers the eggs with straw to hide them. When my broody sets he will set them while she eats and then let her back on the nest. He doesn't attack people. He'll actually...
This could possibly be instinct if you are trying to introduce chicks that aren't his. Have you had the chance to let hens hatch his offspring, or does he kill those too. If that doesn't work maybe let them mature more. Then try introducing them as new hens in a separate run until they are used...