Looks like it could be a fun manga. For once it's an actual villainess, rather than a reincarnator or someone who's just misunderstood, even if she's a bit deflated. Don't expect any hasty progress here, despite the somewhat forceful beginning.
Yeah, misunderstanding someone's intentions doesn't make it rape. It's not like he created the entire situation, nor had he any intent of doing anything with her. She's actually acting with more intent than he did, but she's also misunderstanding that that's what he wants.