Don't do the farm upgrades on the high growth cities like Carthage. Farm upgrades increase pop. growth by 0.5% per level. The base farming for Carthage is something like 14. (Each level increases the count by 1.)

Always keep a spy in each settlement. This mostly prevents bribes, and it keeps enemy spies from reducing loyalty. It also will prevent most sabotage.

Keep taxes maxed out in the high growth cities for as long as possible. This will reduce their growth rates considerably.