@WillLi It's not irrational to use every normal safety measure against an abnormal threat, under the "it's the best we can do" theory. That said, you're dead on about the psychological isolation being completely retarded, unless they're up to something.
@kn1000a I see what you're saying, and you're right - there's an empty niche out there for treating an interaction with another world realistically, because that's usually not done very well. GATE tries, Trinity Wonder tries, Spec-Ops Asuka tries (and mostly succeeds, although it's depicting the aftermath of a collision with a magical world, not the collision itself), but there's nothing that really gets it entirely right.
I'm just irritated about the tone shift being done badly, and I feel bait-and-switched. Even if she's released later, there are still too many elements about this 'quarantine' that scream "none of this is on the level" in an Akira or Elfen Lied vein, to the point where I'd honestly be disappointed if she's just released after they figure out that either they can't do anything or she's harmless by any means they can measure. Having the other main characters contact her via phone from wherever they're being held, or giving her a lawyer/advocate (because she really needs one - not understanding the world and all) would help the realism a lot and dial down the "ah, it's one more Japanese work where the government is dicks" meter immensely.
Because if I wanted to read something about the government being dicks, I'd go re-read Akumetsu. That's not what I come to this manga for.