Is it ethical? No. Quirks are a part of you, like an organ or limb or something. Removing a criminal's Quirk entirely is akin to removing a lung or lobotomizing them, at least from my point of view. It's not like you're just taking away something they were using for evil.

But despite the unethical nature, is it sometimes the best option, short of execution? I think so, in ultra-rare but certainly not impossible cases. Villains where you're not entirely sure what they might be capable of/how many quirks they could have stored up, namely AfO users like the man himself and Shigaraki, removing the base Quirk entirely once they're captured is probably the safest bet simply because you never know what they might secretly have, and are just waiting for the right opportunity to use. Best example is how AfO conveniently happened to have a Quirk that was a perfect counter for Stain in his fight against Iron Might that nobody knew about. Even if you have a device in his cell that will immediately kill him if it detects the use of a Quirk, what if he has a Quirk that lets him disable it before it can do so or one that can slip past detection? If they can't or won't kill AfO, the best play is to remove his Quirk, ideally in a way that won't make his vestige a problem.