How long did you give your roo and hen to get acquainted? It's normal for a chicken that's been around for a while to be aggressive toward a newcomer. Usually it's a quick peck on the head and they settle right down.
Sometimes there could be a fight if the newcomer thinks she doesn't want to accept being number two. But that usually resolves pretty quickly, also.
If your roo saw the hen and immediately decided to mate her, it could have appeared she was being attacked, especially if she objected and put up a fierce resistance.
I would first of all reintroduce the two, but do it more slowly by keeping the rooster confined and allow the hen to explore her new surroundings for a few days, gaining self confidence and relaxing, getting acquainted with the roo through a barrier so she is safe from any aggression on his part.
Watch how the roo behaves while he's watching her. Wait until the two of them are relaxed before letting him out of his cage. Remember, some aggression is normal, but you want to step in if he appears to be doing more than just a peck on the head to show her he's the home boy or grabbing her neck and climbing on her to mate.
