I know there's a lot of problems with visiting a "real" fortress with an adventurer, but in the short term, most of those could be "solved" by simply ignoring them. First dry all the mud and destroy any farm plots, then move everything into stockpiles if there's room, and save all the units and objects. The fort is then effectively put into stasis and nobody does anything other than mill about aimlessly (this includes getting hungry or going crazy), until the fort is reactivated, or an adventurer interacts in some way.
And adventurer can interact with a suspended fortress in four ways: recruiting soldiers for adventure, trading with shops built during the economy, getting quests from whoever is willing to give them, or aggravating the populace. If you choose to retire there, your character hides in the walls until forces unknown call upon him once again, or maybe just sits around as a useless npc during fort mode.
Sure, some people will abuse this to get an endless fountain of iron bars (create character, strip naked, reactivate fortress, melt metal items) or otherwise, but that's their problem. I want to be able to start a city, suspend it, start a mine, abandon that, then haul the bars and gems to the city as an adventurer, extending the life of the city somewhat. Think of it as a kind of primitive Caravans Arc.