I still hate these people with a passion, but at least they've reached the point where they've acknowledged they were the ones who fucked up. They're the reason this boy has locked his heart away from everyone. And the first step in resolving any kind of problem is recognizing that there is one.
As scathing as Makoto's words were, his step-mother needed to hear it. She (and all of them really) needed to hear from his own mouth how much they've hurt him. She was supposed to be a parent to him, and when he needed her most, she turned her back on him. Whatever shallow heartache she's going through right now is NOTHING compared to what he endured. At least she can still FEEL that pain. Not that she's much better, but at least his step-sister now knows to back away and let the guy have the space he needs. Trying to force the 'happy family' act to sweep it all under the rug, hoping he'll 'come around eventually' is NOT going to work here.
As much as I'd love for Makoto to just continue keeping all of them at a distance until he graduates, and then just disappear and go NC with all of them, it's probably going to go the reconciliation route, which is going to be a very long and rocky path to tread for all parties involved.
tl;dr-
That whole family needs to go to therapy. Including dear ol' dad, if he ever deigns to shelve work for a minute and put his parental responsibility where his mouth is.