We've discussed many methods for trying to persuade players to make only a few cities. Here is yet another.
A lot of population growth in Elemental comes from people wandering in from the wastes, not from having babies. People wandering in from the wastes should be driven by prestige only, and they should be split among existing cities. That means that if you have two cities, the growth rate for each city will be cut in half.
This could be balanced in several ways, including having a kingdom growth rate based on prestige and a baby growth rate based on population (although the baby growth rate arguably could be a quadratic - cities historically were very unhealthy places and became more so as they became bigger - much of city growth came from people arriving from the countryside, again tying back to a kingdom based population growth rate rather than a city based one).