I read ahead, and the author actually copped out. Shiho, the girl who pointed Kakeru toward the "Fallen Samurai" was apparently also a rape victim, and one who suffered for it, getting dumped when she admitted it and then having the story spread around school and getting treated like a slut. However, after Kakeru fails to kill the guy, meets Aoi and goes to a hotel with her, it hurts and she bleeds from her broken hymen. Yeah, turns out the guy pushed her down and did sexually assault her, but he didn't penetrate her. The blood as she went home was from her first period, and she didn't connect it because the shock and trauma along with her youth resulted in her not getting another period for four years.
In short, like so very many manga authors, this guy didn't have the guts to actually write his main heroine as an actual non-virgin, let alone a rape victim, and jumped through any hurdles he could think of to create the trauma while still making it so the hero could be the one to deflower her.