Am another one who thoroughly advocates the using of fishing rod toys for wearing out young hooligan cats.
From what you describe of their behaviour, she's not being aggressive per se, just discouraging him from being too "over the top" and it's how kittens and their littermates learn. Sometimes it seems very savage to us, but amongst cats, it's not uncommon.
You could try and make a "path" around your rooms, so that she has places she can climb on to to evade him when he's being too much for his Mum. Things she can climb on to and to progress round the room are great - ie shelves and bookcases (you may have to remove valuables for a while first) and other items of furniture or scratching posts and activity centres with higher paces where she can gain the advantage - on the other hand, if she prefers getting under things, or into things, then think about where you could provide those.
Has Comet's eye been checked over, just to make sure there's no serious damage?