A prison labor camp would be a better level than a prison, I think. They contain quarries, factories, farms, little outdoor huts as living quarters, etc... they're essentially small village on total lockdown. Seems perfect for a Hitman level and gets around a lot of the worries... you'd get a prison that is structured more like Sapienza than Bangkok. Here's a link to the labor camp level I wrote up a while back.
I really don't like the idea of 47 getting intentionally captured and then having to break out. That is such an awful cliche. There was one summer where three of the blockbuster movies featured major villains who did this as part of their plan (Avengers, Skyfall, and something else I forget). And then soon after a bunch of games came out that had you intentionally getting captured then breaking out. I rolled my eyes at Watch_Dogs hard when that game made you do it. There's nothing intrinsically wrong with the idea, but at this point it's so incredibly unimaginative and hackneyed that I'll be disappointed if IOI goes that route.
Still, I can understand the appeal. Anyone know the story arc in Daredevil comics called The Devil in Cell-Block D, written by Ed Brubaker? It's great; you should seek it out if you like comics. Matt Murdock and the Kingpin are both locked up in the same prison, so Bullseye and the Punisher intentionally get themselves captured so they can be a part of the mess, and you've got a superhero comic that plays out entirely in a prison. It's excellent.