Like Macedon stated - exterminate them!
For a town under 6000 pops I keep 2 garrisoned units plus the commander. For 12000 I keep 4 etc etc. If the city outgrows me like you describes I build one peasant each turn for a couple of turns and when the loyalty no longer can stay above 100% on low settings I pull my troops out, 2-4 troops plus 4-6 peasants, and set the tax slider so that loyalty is 0%. Let is rebel and retake it. Before you take it though you can pull out commanders in cities that you don´t want to get the pop-boom from enslaving the rebel town. If exterminating there´s no need for such action. Don´t use a general for theese clensing(sp?) operations. Oh! I actually auto-calc theese since I find it tedious to fight a battle with peasants and it works great!