Thanks, this really helped me understand what was going on in much greater depth. It's really telling that Mitsuki's opinion of Ayaka doesn't seem to change once she has context for what she's been doing. The last line really stings with that in mind.
It's interesting re-reading the story with that context. Ayaka seems to see their connection as something like partners in crime or co-conspirators, and she clearly has some standards for how she governs her pursuing of men. Mitsuki, meanwhile, doesn't understand this, and sees her as a friend with an attitude towards dating that she disdains. When Mitsuki disguises her affections by acting like someone who just thinks flirting is fun, it's like you say--it hurts Ayaka, and she pulls back. It makes me wonder how things would have gone if Mitsuki was honest that she did it because she wanted to spend time with Ayaka. I feel like that would have really changed the context of Ayaka learning definitively that she isn't serious about pursuing guys--like, she knows they're not in the same situation, but maybe they can be friends in different places supporting each other. It's cool to see someone being dishonest about their feelings punished this harshly in a manga.
One part I still don't get though is what happened in that whole scene after the big reveal. What does she mean by, "so that's the kind of girl you are"? Is Ayaka blushing because Mitsuki is turning her on, or is she ashamed because she's being pushed to present information she doesn't want to in an effort to protect herself? Is this kind of a complex cute moment between them, or like hella non-con?
I do think Mitsuki's opinion changes somewhat by the end. Look at how she's saying it, with a big grin on her face. Even if she still thinks that, the emotions surrounding it are different. Some of her disgust towards Ayaka was probably jealousy: she didn't like seeing the woman she loved chasing after men. Now that she knows that Ayaka wasn't having sex with them (and now that she herself has taken Ayaka's virginity), she's no longer jealous. And maybe it's also her way of saying that she understands what kind of person Ayaka is better, and realizes that's part of what she loves about her? It is the first time she's actually said it out loud to Ayaka, instead of just thinking it to herself. It's a very strange thing to say to the person you love after your first time having sex. But it does feel like a very fitting ending to this story.
I also wonder about that part where Mitsuki lies to her. I do think Ayaka is upset mainly for the reason I said before, but maybe this is also mean to indicate that, consciously or not, Ayaka is aware of Mituski's feelings and returns them? There was a lot of emphasis on the way Ayaka keeps touching Mitsuki leading up to this. So perhaps she wanted to hear Mitsuki say it, and was disappointed when she lied instead.
As for whether it's rape, I personally think that the art and story indicate that Ayaka is into it? My interpretation is that she's blushing partly out of shock, partly because she's embarrassed at revealing that she's actually a virgin despite her posturing, and partly because she's turned on. I think especially her expression on page 245 indicates that she's into it by that point. But the whole situation definitely feels more than a little rapey. And the part where they actually get undressed and have sex is left to the imagination, so maybe it's meant to be ambiguous?