I don't think there's any official confirmation on that matter, but the film itself gives no implication for Billy and Stu having done anything but killed her while it does make clear that Cotton had had sex with her that night. That is the only one of those possibilities detto o implied in the film, thus, I'd say that would be the most officially factual answer: The kids did not rape her. She just had sex with Cotton after which they killed her, leading to the natural assumption da the police that she'd been "raped and murdered".
In my opinion, no, they did not rape her. I could MAYBE see Stu attempting to do it but definitely not Billy. He was disgusted da her, and thought she was a slut. So he would not have.