Your son needs help. But at the same time your daughter needs to feel safe in her own home. You could try talking to a psychologist in your area and maybe see about getting him sent somewhere for juveniles. If you want something more done as far as charges or something call the police. I really dont think your daughter should have to live with him.
For you to abandon your son so easily, I suspect that you have been having some sort of trouble with him all along. If so, what is the nature of those problems and how have they been handled? Where is his other parent?
Did Child Protective tell you the reason why he wasn't to be removed from home and away from his younger sister?
I am surprised that they dint do more if he raped her, she is under age this is statuary rape...I suggest you ask the CPS why ,it doesnt make any sense can you give more details .....she shouldnt be near him, and I would have expected him to be charged with something ???