I really don't believe Tsubaki was raped, though I do believe she was touched in a sexual way, made to expose herself or otherwise place herself in a humiliating position, as part of a failed blackmail scheme; she might have even been battered. Literal rape typically would not leave a woman in a state to which they would further desire sexual contact, as she has been for some time now (no hentai logic in this series). Plus, the school doctor would definitely be more cautious with her during their Q & A session about masturbation. Her knowledge of anything sexual is so limited that it would be a far fetch to explain that she had actually been forced to perform any sexual acts. No, I think some guys got handsy with her, forced her to strip, and perhaps smacked her around; it's quite possible that Tsubaki's defiance is what saved her from being fully taken. None of that is good of course, but this series would certainly take a much darker turn if something worse had happened to her, and I don't see the author moving it towards that direction.