That's just it.
They aren't bad guys.
They are just antagonists who are taking a powerful potential threat to the entire world away from people who have shown that they have no idea of what they are doing with high tier quirks.
Leaving her in the hands of people who are still playing the superhero super villian game would be a great threat.
Can you imagine Eri wanting to be a heroine and using her powers randomly and without thinking about it beyond beating up da bad guys?
The only persons on the earth who have a decent understanding of quirks are the evil doctor what's his name and afo.
That's about it.
Think about having someone with that level of power being as half assed in her control of power a the normal superhero.
An organization that knows that there will be god level quirk users born occasionally and take steps to procure and train them/take them away from the rest of the world makes sense.
Espescially since hori has dropped the each generation is more powerful bomb. >>190730976
Eri kidnapped by quirk illuminait
Mirio tries to fight them but is bodied by a quirk user that is a jean grey tier telekinetic. Eri uses the last bit of her power to give Mirio access to his quirk...kinda.
He then takes eri into a portal that the woman who is casually standing there opens.