Unhappy population

[Brutus]

One option if you're already stuck is to let a city rebel, then take it over and exterminate the population.

Better still, take your garrison out of an overcrowded city, gift the settlement away to one of your enemies and move the garrison back in. You'll be given the option to exterminate or enslave again because technically you conquered the city, though because there was nobody to defend the walls you don't have to actually besiege it and lose troops or anything.

It isn't really fair, but it works quite well.