Not sure why this got kind of overlooked, but this strikes me as an excellent solution. When monsters invade, have them turn your former city in to their new lair that must be liberated. Even have them start spawning raiding groups over time if it is ignored.

Once you get the city back, after a repair cycle, the city itself is still functional and just must be repopulated. Certain monsters/events can still completely sack the city when the context makes sense.

Wait until I publish my Population Mod. It will do exactly this. Currently I am having some difficulties with the part of adding upkeep to units, but the part of requiring population to run buildings works perfectly

Monsters go to town to dine:  they eat their fill, and leave...(if they kill all their 'livestock' there will me none available when they are hungry later).  Game effect: monsters go into town and consume 'some' of the population, and destroy (some) infrastructure. They leave, and wander around (or go to their lair) sated for a time <insert sated time here>.  They will be back to nosh on the residents again later.  Humanoid 'monsters (like bandits, maytrs, etc.) go to town, raid, steal, have fun.  Again, destroying the settlement also destroys future food/fun/etc.  Game effect:  humanoid monsters damage settlement same way monsters do, OR, instead of killing (dining on) population, they 'take' resources that allow them to upgrade their weapons armor and increase the size of their band.  They leave for their lair for a <inset time frame here> set amount of time.  In either case, unrest increased.  Game play intent:  Player now has option/ more time to rescue the settlement, and go after the 'monsters.'  But damage is done.  Perhaps the 'maytrs' do go in and kill them all.