I honestly find it a bit surprising how some viewers of this anime have an extremely hard time imagining that the scientist class could do something ethically questionable and oppressive to some people.
Fiction is loaded with villainous scientists who do generally villainous things. The term "Mad Scientist" didn't start with Okabe Rintarou...
And even putting that aside, I think that many perfectly sane and reasonable scientists would prioritize the survival of the human species above just about anything. To that end, it's not hard to see how they could rationalize (to themselves) tightly controlling the world's PK population through the setup that we have in this New World in Japan.
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