Couldn't we just increase the weight of oppression that city units impose to prevent flips?..You are right on this, and actually it had already came up a few weeks ago. The suggestion was something like this: When cities flip, there should be a cap that only 3-4 units flip with it, the others are moved back to your nearest tile
A lot of the conquest Civs would benefit greatly (read: me when playing them

Shouldn't impact the new historical flips as they are using a separate mechanic I think.
Depends on unit maintenance I reckon, needs to be high enough avoid cheezing ones way through world domination, hmmm .. maybe a limited unit loss on flip is better.