Sure bud...But spoiler ahead:
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As of now, with all of the clues in the game, I think that she is not affected physically...to the extent of what you said, "raped". The only thing is that that penis spider released the gooey stuff on her breast - and as Meave said, that somehow kicked off the pregnancy procedures in Mia's body. But again, as far as "physical stuff" goes, Mia said to the MC (you) that she has only touched herself while watching hentai. She did not even have sex yet lol!