well how bout this, like a good persistant world, the mayors and such would be voted on by the players, and only that person would be allowed to que work orders and designate buildings/mining. Only after being designated would the Regular players actually be allowed to work on said areas. Perhaps certain NPC's could be generated such as Gaurds/wardens to stop players from being OVERLY idiotic, which would punish the normal list of law givers, and considering the intracacies and random idiocy of noob players, they would not be able to stand up to the awsome might of the all mighty hammerer as he draged them to his cell to await the logging on of the mayor/King to decide his punishment.... overly noobish players would instead, be dead from hammer strikes ^^ god bless dwarven justice!
Of course to prevent endless wars and over powered i beleive all the normal creatures should run as normally, no player ran broze collosi etc etc, the possibility of a succesful fort being able to capture and tame a roaming dragon and using it in their war would eliminate the constant siege halting trap lines, and perhaps each race would be able to hire mercanaries and NPC creatures at certain stages, in particular the ones they normally use. Dwarfs might need some editing, but goblins bringing along Trolls would already be expected, and with them being building destroyers a similar destroyer creature would have to be a mercanary/creature for hire by each race. Not to mention siege engines would need to be workable at this point and time to to prevent the "OMG its DEVONUS"S ARMY OF DOOM< BUILD A WALL, HA HA, you can't get in......"
then again, with some members of the army being player characters, its actually quite logical that they could be used as sappers to penetrate the enemies fort, but with them dieing and the enemies army promptly repusling the intruders and building a wall in the gap to stop further threat from that section would lead to some very dynamic, and even fort ending battles.
"Yeah, they can't get in, i have 1000 traps in our only entrace way...... wait what? what do you mean they just broke into our booze stockpiles on z-level -3, what do you mean they let a dragon in?!!?!?!?! WSAVE THE BOOZE!!!!!!!" this could lead to some very interesting fights, fort ending sapping operations. actual siege like battles as the defenders inside rush to plug the wholes and protect the food stores while they await aid from any ally, and the attackers trying to breach walls and devise ways to end the fort.