How big is your coop and run? Is the pecked one acting sick or odd? How old are they?
I would remove the rooster and see how the hens get along. If that doesn't improve things, than I would try removing the bully hen to see how the rooster treats her. You may need more hens or one less rooster. Smaller flocks can have more aggression because there's less birds at the bottom, and in your case there's only one.