Mind that i've been stating these in the context of the fact that dwarf mode, and sites in general, have personal sovereignty, and looking forward from the current framework, unless you made your site under the specific direct authority of another site (unlikely, Slaves to Armok and all).
I imagine there could be specific embark modes and scenarios, but what i'm stating is an actual outright functioning fortress could, at some point during their flourishing, decide to build mass-prison facilities and begin make diplomatic discussions with groups who need the prison space.
Saying that you "lose the fortress" outright in this instance because it's both illegal and unpleasing to your head civilization is completely out of question with how Dwarf Fortress is to be played, it's like getting an instant game over screen if you dump a dwarven caravan into a magma pool out of spite or whatnot.
If your parent civilization wants to shut down the site, I'd like to see them try. Actually try. Insurrection, siege, withdrawl of funding, etc. And whether they consider this in their interest to even bother due to outstanding wars is also another question, too, considering that with enough social isolation and management to prevent insurrections, careful or hermetic defense setups, and the like, the player generally is (and probably should be) capable of defending themselves for quite some time, even with new siege diggers, given enough preparation, and fortresses are often able to dig their heels in well enough with enough farming set up or large enough stockpiles.
If the prisoners riot, then your control of the fortress is basically considered by what dwarves you have alive. If all of your dwarves are captured, defect, or are killed, then you get a lose the game, practically like you normally would.
I had figured that prison sites weren't -just prisons-, but rather, nominally, a normal dwarven fortress, by gameplay and situation standards, however, with the exception of:
-Implicit specialization by the player to construct prison spaces and to buy/grow enough of their food to support prisons. This isn't strictly necessity, either way you cut it, but hinders the latter point if you don't do it.
-Contractual agreement with other civilizations or groups, or on your own auspicions (if applicable), to import prisoners.
If prison starting scenario means we are just going to get prisoner contracts, then why not just have us build the prisons ourselves in the normal fashion in a normal site and then have nearby sites respond to our large, spacious prisons by sending us prisoner contracts. Having prison fortresses function in gameplay terms identically to regular fortresses makes the whole idea completely redundant, I think the idea of starting scenarios is that they have defined citizen statuses, so guard VS prisoner determining gameplay options.
Like i've said, imprisonment offers would not be strictly scenario-only. You would be allowed to show off your prison spaces to diplomats, or diplomats could get the good idea of asking for said offer, and such agreements would be handled similar to how diplomacy currently works.
Then we have a list of local citizen statuses that are found only in the starting scenario itself. In this case the guard status has no requirements, save not being a prisoner, meaning that everybody who freely immigrates into a prison fortress automatically becomes a prison guard, even if they are not presently doing any guarding. What makes the scenario a challenge is that the guards do not work as discussed above, forcing us to use the prisoners as labour; which means we cannot simply leave them in their cages. However with non-civ level citizen statuses it would be possible to set a timer on their implementation, so it is 6 months into the starting scenario not immediately that our dwarves become officially guards and stop working, hence some of them can build the prison.
Forcing statuses like this is particularly the reason why I'm suggesting against scenario-mode-locked prison fortresses. Normal player made fortresses can do the job well enough with less than half of their population being in the military, anyway, no?