I'd say debatable. That character was, on all accounts, trans to begin with, so if we're talking technicality, the change was driven by the desire "she" had to be a woman. So in that sense, is it really a matter of the MC willing the change all of his own accord or more the intent of the person he was using his power on... I'd say more likely the second. After all, is the prisoner had been against it, it's likely the body the MC was trying to change would have resisted.
That's all true. But you also know that there is definitely something bigger shaping up, something she knows about. There's been enough hints and we've talked about it. So even if the MC didn't ask for shit, taking into account that point, it's very likely she's doing it with pretty much all her pupils to, one, make sure they get strong enough to not get wiped by the first monster or HERO grunt to come along, two, learn to control themselves instead of letting their inner monster win, and three, possibly become strong enough to resist/help in whatever is coming.
Should she have rather explained and recruited volonteers ? I... don't think so, actually. That wouldn't be a good way to get people with an actual chance and the will to actually push further. Rather, she'd have ended up with people wanting to play superheroes or getting power for selfish reasons becoming nuisance for her plans. Plus she could have been rated out to HERO.
Also I don't think the MC would have progressed that far, or that fast, without Ella putting her fingers in that pie, honestly. She made sure to give him a steady line of hurdles, while he would have just likely enjoyed his student life using his powers for nothing more than be a huge beefcake with a massive dick.