These kinds of situations are never simple or easy.
Most important of all, on the bottom line, is that you need to do what is right by you, morally and ethically. If you are not ready to forgive her for this, then you are not ready. If you do not want her in your life because of this, you don't want her there.
That said, if you think you can stomach it, as long as your uncle is not around, I do not think that she will be a danger to you or your children. If she has a good relationship with your children and they might be hurt by never seeing her again, it might be something to consider toughing through family gatherings that she is at, even if you never invite her to your own home or allow your children to go visit her without your direct supervision.
While I think most people would disagree with the choice she has made, she isn't in an easy position either. A man that she loved and promised to live her entire life with and had children with is not the person she thought he was. As healthy as it might be to cut him out of her life and move on, not everyone is that strong. I just hope that her daughter does not suffer the same fate as your cousin.
I don't think there is anything wrong sending an email to her stating your concerns. At least on my end, I like to be dealt with straight up. I don't like it when people just drop out of my life. Even if I can probably guess the reason why, I don't like to do that. I like to know why someone has chosen to remove me from their life. That way, even though it hurts I can move on and stop wondering what happened. The way I see it, you don't need to be cruel to firmly state that you do not think you can abide by her decision and that you wish to discontinue her acquaintance with you and with your children unless and until she is no longer with your uncle, that you understand that this situation isn't easy for her, but that you do not think it is healthy for your family to be around her or hers in light of the events that have taken place.
I'm very sorry that you have to go through something like this. I've never had any molestation in my family that I know of, but I can't imagine how I would feel if I found out about something like that. I hope that your cousin is safe from her father and I hope that no one else gets hurt due to this situation.