Again, I play on VH/VH/huge units and I’m not having this problem. I played the Brits last, who don’t have a lot of joy-joy buildings. I almost always exterminate a large city upon conquest. Remember, Caesar killed perhaps millions of Gauls. By shipping my peasants around I was able to keep a lid on population growth in problem settlements. Just ordering up a full row of peasants takes a couple thousand citizens out of the population. I think that the best advice is to be quick in your plan of conquest. The longer the game lasts the larger your settlements will become.