The character assassination will probably work, at least for a time. She'll have trouble finding artists and riggers willing to work with her if they want to also work with Nijisanji, she'll lose a few friends and collab connections for the same reason, and she'll be dealing with swarms of kpop teens doxing and flagging her for months, with possibly years of low-level spam from them. Eventually she'll recover somewhat, but never fully.
As for NijiEN, the damage will be harder to detect, but arguably more acute. Maybe even fatal. To anyone who isn't a they/them debut TBA vtweeter, what this incident says, regardless of what you think of the termination, is that if you work for NijiEN and you ever get on their bad side, they may absolutely drag you, publicly shittalk you, possibly even leak your personal information to stalkers and harassers who are somehow able to be worked into a blood frenzy on a moment's notice, and you won't even be able to give your side of the story due to NDA. They will see fewer and fewer competent indies with a healthy level of caution apply, instead getting wave after wave of vindictive weirdos. To the clique, this will seem at first like a win, as the indies orbiting the clique will have less competition and they'll stock the ranks of the branch with more and more people exactly like them. But this will only be piling on more and more risk of backstabbing and public breakdowns.
More crucially, however, is that this will fuck with Anykara's business model. Their strategy is simple, but effective. Criticize them for "quantity over quality" all you want, but the sheer number of vtubers under the Nijisanji brand means that there's someone for every taste. Whole swathes of NijiJP rarely if ever interact with each other, and their fans can be similarly isolated. And when they want to collab, being under the same company makes that that much smoother. NijiEN never quite managed this strategy properly to begin with, but by filtering new applicants to only people on the clique's side, they may have completely killed it. And if that's the case, new waves will just be more and more of the same audience spread a bunch of low earners. Will the branch survive that when Anykara has to answer to investors? Maybe, but the branch would have to be practically gutted.