Yeah, solitary confinement is pretty inhumane. Combine that with a tiny cell, nothing whatsoever to do, no contact whatsoever with the outside world, etc. and it's about 3x worse than the worst prison. That's pretty fucked. I am sorry, but all these characters would have a huge ethical problem with this in real life, and while I can usually let a lot of stuff pass, this one annoys the hell out of me and it's all I can think about when they are down there or going after a meta human. I don't care about the alternative or them being dangerous, it still doesn't change the fact that these characters, these people, basically anyone but the worst and most extreme Nazis, would never really inflict this kind of treatment on any living thing. One single line about rehabilitation or just even that they can't keep them locked up forever or hell, even have Cisco bringing in a bunch of books for one of them, just let the audience know the team aren't a bunch of sociopaths.
Also, how dangerous is some vulnerable, gullible young thief girl? How about compared to someone that has been locked up unjustly in inhumane conditions and then gets free one day? They are going to care only about a single thing the day they all get out at once, and it's gonna happen. Annnd if that's why they are doing this, that is lazy cheap writing.