Firstly I'd cut her nails very short and file them so she can't scratch any more. We file DD's nails so she can't scratch her eczema. If there is no white left she can't scratch. You'll have to keep on top of it. I can't do it myself but dd doesn't wriggle so much for dh.
You dd may be very good at talking and understanding for her age but she still has the emotional maturity or a 2.5yo. Scratching has obviously become her thing that gets a response and it's hard for all of us to change patterns of behaviour so don't expect any quick fixes.
Firstly, when it happens during play, thats it, game over. I wouldn't let her see that she can re-enter the fun after hurting someone. I would give my attention to the other child by comforting them. Then I'd tell dd 'that really hurt your brother, can you imagine what it feels like to be scratched like that, no wonder he is crying, I don't think he wants to play with you any more'
Incidentally, I don't ask my children to apologise (unless it would be really rude not to ie an old lady in the street etc) instead I apologise on their behalf. When dd was small I didn't like her being forced to cuddle the child that had hurt her because their mother told her to when my dd was normally still scared of the bigger kid (to basically make the mother feel it was all ok again). and I don't like seeing kids reeling out 'I'm sorry' when they clearly aren't. Mine do say sorry when they feel sorry about something and by trying to bring them up with morals they'll turn into people who aren't just sorry they got caught etc.
In the rough play example you give it sounds like she didn't mean to hurt her brother. It was done out of habit.
It sounds like its the doing it out of anger that you are really bothered about. How about suggesting she does something else when she is annoyed? stamps her feet? When she is obviously annoyed, show her how to do it and get her to stamp as hard as she can and get it out of her system?
I would also try to let her feel she has a bit more control as it sounds like she gets angry when things are being done to her. ie if you are holding hands, tell her 'lets go this way to go to the shoe shop' rather than just head there. Give her lots of time to get into the car (via playing around the garden etc - they do things sooooo much slower at this age) etc.
If neither you or her brother are really in to rough and tumble, perhaps she isn't getting enough to satisfy her? Have you tried letting her tickle you or basically be in charge of some rough play? You have to play along as its not nearly as fun as you have to let them think it is. Sometimes they just need to get toddler aggression out of their system.