Can't take it anymore

[Asmodai]

Good points Asmodai, I must admit that that I would perhaps differ with respects to enslavement. This tends to grow the populations of all your cities, adding to the problem. I only ever exterminate.

Also I tend to avoid the sewers line of buildings as the public health bonus from these also boosts growth. I also avoid building any temples that give population growth bonuses and only build the first one or two farming upgrades. If you're going to go with a policy of extermination then there is no sense in trying to promote growth or contain squalor once the settlement has gone above 24,000 and been fully upgraded.

Exterminations in every captured settlement can leave near all your conquered cities without manpower to replenish your armies.
But it is good thing to do that in settlements, that you dont want to expand at all. Also, enslavement raises population not in all of your cities, but only in thouse cities with governor(probably 2-3 most advanced cities, that occasionaly needing population boost for recruitment of most advanced units), so it is not a problem. Most of added population will be used for troop production.
I agree, that too much population buildings in too much cities is bad thing. Concentrating on few, chosen cities is always a good thing.