Look, I guess it's possible Suzune got raped by Kanemichi in the time we don't see her, but by the way everyone is relatively safe in the good ending, I strongly doubt that was the writer's intention. Also, let's be honest, Suzune agreeing to Kanemichi's rape is definitely the dumbest choice in the game, she has no good reason to agree, or even trust Kanemichi's obvious bullshit. Yeah, it's possible she got raped, and then defeated Kanemichi, but that happens nowhere in the story, nor is it hinted at, leading me to believe Suzune defeated Kanemichi without much happening. Now I will admit, the time Suzune takes to get back to the main storyline is suspiciously long, but I feel like it's more lazy writing than intentional. But, hey, if your perverted mind wants to believe the worst happened to Suzune while she's offscreen, let your imagination go wild. XD