I don't like the idea of a quirk-remover myself, especially if the PCs would then inexplicably be shielded from such removal due to plot armor and shit. If they have no more conviction than trying to make humanity as a whole quirkless again, I feel like it'd make most sense to go after the younger generation rather than established badasses, especially if the targets have to be subdued for a long time.
Which is sorta horrible and gross too.
Well "plot armor" would also apply to character being killed. That's why I would imagine there wouldn't be plot armor established in this RP. All characters would be equally susceptible to becoming targets if the characters take reckless risks if they encounter the "Big Bad".
The most hard hitting points of BNHA was when Deku thought he was going to live a life without any powers in world full of super humans. Within the universe having a character that could remove your powers and make you "normal" would be horrifying for students of UA. Students who whole hearted desire above all else to become Heroes.
And making him needing to bind his targets makes it a little more terrifying in a way. Like as if a giant spider was slowly wrapping you in its web before feeding. And while "horrible" and "gross" it's a point to make him all that more Villainous in a way. Not only in action but in function.