I think what you are doing by confining them, is a good idea. You may also enlist her to help you take care of them. Under close supervision, she can help you clean litterboxes, feed and groom them. This may also help her bond with them a little more. If she is good about helping with them, then she can give each cat a pet (while you watch) and if the cat will let her approach them, or she can play with them with a feather toy for one minute, etc. Essentially, you give her many short, supervised visits with the cats to train her how to be around them, as well as teach her what owning a pet is all about.
I would also talk to her about WHY she hurts them. She may not honestly realize that what she's doing is harmful to the cats. While she may be nine, in my mind that doesn't mean she's old enough or developed enough to really understand how to be with animals.
I've worked with lots and lots of kids, especially those in the 7 to 11 age group, and some of them are just not aware of how to control their bodies and their actions, or how their actions effect those around them. This doesn't mean they never will, it just means they're developing a little slower than other kids.
I agree with getting an assesment as well, as things like learning disabilities, ADHD, ADD, or innability to deal with stress and emotions can all make it hard for your daughter to understand why her actions are innapropriate.