The thing is - everything you said is true in reality.
But your last sentence is the key point, and the reason we the readers are being asked to engage with the work as it is presented.
Ideally IRL Miyuki would get some form of help and not be perpetually punished as she is. But this isn't IRL, and so she is beholden to the rules of the world the author has created.
And for the record - she didn't make "a" mistake. She realized into the two days of bullying that her childhood friend was being tormented, and did nothing out of fear of being subjected to similar if it got out she straight up cheated on him and then lied about him abusing her.
She had the image of "pure good girl" going into that school year and was afraid of losing her street cred in her class.
She also knew, at multiple junctures, that what she was doing with Kondo was wrong--all the way back at even agreeing to meet him at the suggestion of her friend. But she liked the sex, she liked the immorality of it all, and she thought so little of Eiji that she convinced herself he would forgive her because "I'm special to him".
Yeah. She's a teenager. But she absolutely made a whole series of choices that push far past "mistake". And again, IRL? She should be afforded compassion after a point and help.
But not in this universe.
I am starting to see why do you think what do you think about other series, if you believe Miyuki was just an accomplice of the torment. She supported actively the account of Kondo, she even left Kondo punched her and taked pictures to give "proofs" of the supposed mistreats of Eiji. So, yes, she is an active guilty from this moment of his attempt of suicide.
Even the typical NTR girl at least would try to protect her cucked boyfriend from these kind of vile accusations, even if would be in mode "you are strong, Kondo, he is weak, he is too pussy for that, he has not the balls to harm me, doesn´t bother with him, the strongest doesn´t bother by the weak ones like him", like Catelyn Tully defending the life of Petyr Baelish in precisely GoT/ASOIAF.
Anyway, I´m agree with the comparison with Theon Greyjoy, other fucking asshole, but even him didn´t deserve so suffering.
The best for her definitely would be go look to other city and start again from zero.