A Trek "prison," which would actually be some sort of rehabilitative penal colony with few, if any, similarities to today's prisons, would probably not make a fantastic setting for a drama. By our standards, it would probably resemble a lot of touchy-feely group-therapy sessions and outdoor work on art or tending animals and stuff like that. There's so little crime in Trek and so many of the serious crimes appear attributable to mental illness that I don't know what sort of people you'd really be seeing in these facilities. Imagine a bunch of people like Bashir's father or Tom Paris, who made bad decisions and copped to them, and I suspect they mostly sit around brooding over their sins until they reach a point where they decide what to do with the rest of their lives. I imagine the mental institutions of the Federation might be a bit more...exciting.
That bit about the female Changeling standing trial for war crimes didn't make a heck of a lot of sense to me. What are they really going to do? What is achieved by keeping her locked up? I imagine they just had her sign a bunch of BS responsibility statements for the history books and then released her back to the Dominion.