My EE (hatchery Ameracauna) has always been the lowest in the pecking order, too, even though (or maybe because!) she is the sweetest bird. Separating her is the right thing. Good luck!
from Ohio. Blue-kote and separation until she heals. You could also put another pullet in with her, to keep her company. I would gradually add another one in with her every few days-if all is going well-until the only one left is the bully. Keep her isolated for several days (even a week), so she wants to be with the others, and then see how they do together.