you can just demolish the basic housing (and get the food back) and replace them with your houses, viola the perfect city
I do exactly that, Tesb. As I said, it's more a nuisance than a counterbalance.
Regarding a possible solution for the general problem? How about a "assimilation period", while you "reeducate" or "integrate" the conquered city into your empire. [Yes, I know it sounds horrible, if you image it in a real-life context.]
During that time, e.g. determined by the population of the city and its number of buildings, you would not be able to build or train in it. And after this interval is over, buildings would change to their counterparts or be torn down if unique ... or more ideally "abandoned" with extra building graphics. But that would just be the icing on the cake. And of course, should the city be reconquered during the "assimilation", than it would just remain as it was.
Rabenhoff