Definitely give CPS a chance to do their job, rest assured they are taking the appropriate steps to assure the safety of your granddaughter. However, you should also file a police report. I would try being a bit more assertive with the school. If they still refuse to change her classroom, you should consider switching schools. Speak to the principal and DEMAND your granddaughter be put in another classroom.
Just so you know, there are also many resources that will help children who have been sexually abused (whether by an adult or another child), where she can get some counseling for little or no cost. I would definitely recommend you look into this.