There IS a gameplay problem with the incredible rage of rebellion of cities.
Slaughter is required if you want to play without too much of a headache. Not doing it is asking for trouble.

A large/huge city, if not slaughtered, is nearly impossible to keep down when you take it. The unrest + culture penalty + squalor + distance to capital make it so that even with low taxes, a good governor and 20 troops, it still barely hover above 75-85 % loyalty. If you ever need to move some troops or your governor, or after a while due to population growing, well, you have a riot on your hand.

Slaughtering cuts the population, the culture penalty and increase the garrison effect.

I hope this will be adressed in a patch, because it's one of the worst problem in the game, to be REQUIRED to kill everybody (just like in Civ3). At least, there should be some kind of penalty to make other options more interesting (unhappiness problems in the whole empire due to draconic rule ?).