Just for the record, a good alternative to exterminating your populations would be to enslave them. That way, at least your smaller cities will grow faster. Or, if your problematic huge city isn't a military production center, you could try making peasants in that city and moving them to other settlements, disbanding them, and thus causing those settlements to grow (this avoids the hassle of getting an army to a city, letting it revolt, sieging it, then killing/enslaving everybody). The only disadvantage to this is you don't get the bonus from looting your city. Also, every time you exterminate or enslave the population of a city, that city has a population boom. This increases public order until the boom is over, but it also usually means 5%+ population growth, which quickly gets you back to where you started. Also, unless it's completely vital, avoid building the pop growth increasing temples. Once you get to large city they become useless, and making them Pantheons usually has significant disadvantages compared to the other temples. Often underrated, Public Health increasing temples are probably better choices than population growth increasing ones (as public health inadvertantly increases population growth). Odeons, Execution Squares, Taverns, Arenas, are all vital to keeping cities under control. I've had cities with nearly 45,000 people still growing, completely happy, and MAKING money (granted it was Athens and my capital). You really just need to take the time, and read and understand what everything does, how it affects pop growth and public order, and using common sense from there. (On a side note, I think any really populated city that stays happy for a while gets a plague to minimize the population. It's never failed that when my cities are approaching 45,000 citizens, they always get the plague.)
We are all in the gutter, but some of us are looking at the stars.