Yea, the theme can be disturbing, but if DF is part of the inspiration I think that's entirely appropriate. Dwarf Fortress is a deeply disturbing game. I've seen things happen in that game that I don't even want to repeat, they're just so emotionally wrenching and awful. Largely because it made sense that they could happen, given the premises. If it had been obviously absurd it wouldn't have had the same impact.
Actually, that's part of why I don't play DF anymore, though I might give it another go after the next release.
All that said, coming face to face with those situations in that game certainly didn't encourage their
emulation, quite the opposite.
A game about prisons could go either way, in terms of how the player winds up feeling about the overall concept. The developers could spin it either way, or could just try for a simulation where the emergent result is sufficient (as in DF, where I'm quite sure Toady never specifically intended what happened in my game to happen). Imagine how a sausage-factory-simulator game would go; I certainly wouldn't take it for granted that it would be favorable to the subject matter.
On the surface, it is odd to me that Prison Architect would be disturbing where Dungeon Keeper would not, but on reflection it's understandable: Dungeon Keeper glorifies some pretty awful behavior and says "Evil is Good", etc, and it really keeps the mask of really-meaning-it on the whole time (iirc), but underneath it's obvious that it's not serious about it, and no one without a preexisting problem would actually be encouraged to think the things happening in that game would be a good idea to propagate in the real world.
That said, I don't play DK anymore either because the theme is just too overflowingly contrary to me, as much as I loved the gameplay structure itself.
Though something tells me that if Prison Architect were presented with DK's over-the-top "you are the bad guy" mentality, Wingflier wouldn't object nearly so much to it
