It isn't that simple; Honjou very well may be skeptical that he was unwilling, I think she already felt threatened by the Pissbomb-Predator-Sensei. Even if she were to fully believe him, it's still something that's bound to cause friction in any relationship, let alone the first romance that two teenagers are experiencing.
There's also the added caveat that Honjou sort of sexually assaulted him as well, that one time, when he was tied up and she was grinding against him while he was telling her to stop, but I feel like the manga sort of forgot that happened.