I think the most easy fix to implement would be a Traffic Light strategy, during peacetime.
greenFirst time a city would culture flip you should get the message;
"Disident groups are campaining for incorporation to the (whatever civ the flip would be) (whatever their Government is), word is they admire their culture"
and the city should go in to disorder.
Orangesecond time the city would flip you should get the following message
"Ethnic (citizens from whatever the enemy civ is) freedom fighters from (the city) have attacked (your own civ) government officials in open rebellion."
and some of your own nationals should be elliminated, and the happyness improvements in the city should be destroyed (temple cathedral etc..).
Red The final time a culture flip should happen the following message should be shown;
"Armed rebels in (the city) have revolted during civil demonstrations and our own troops have been expelled with heavy casualties, (the enemy civ) has incorporated the rebels in to thier (whatever their government is)." the city shoud flip to the enemy, and your troops should all be expelled to
This way each time the chances of further flipping becomes more likely, Disorder, reduced loyal citizens and finaly reduced happines and culture- This is very much what happened during the run up to WWII on the Czecheslovakian borders.
But it also allows you the opertunity to reinforce against the chances by rebuilding improvements and stationing troops there. It also means that the whole process is more of a gradual slide towards cultural incorporation, rather than a sudden flip.
During a war time the same could happen but with the following texts
green "(whatever the enemy civ) Nationalists are staging strikes against the occupational government"
Orange "(whatever the enemy civ) Rebels are exeqution terrorist actions against the occupational government. Some of our officials have been killed, and relegious groups persecuted".
Red "(the city) has rebeled agaisnst the Ocupational government and allowed (enemyciv) troops in to the city at night. Our troops have been expelled with heavy casualties".
The same should be the case for A.I. cities, so you know there to target your cultural infiltration strategy, for example;
Green "Disidents in (the enemy city) are campaining for incorporation in to our (our government type)".
Orange "In secret arangement with our government (our civ) nationalist militants in (the enemy city) are staging paramilitary actions against the unlawfull ocupation by (the enemy civ)".
Red "Armed rebels in (the enemy city) have thrown off the (enemy civ) tryrants and want to join our (government type), What shall we do?"
I think this Traffic light aproach is the easiest overhaul to make, the most difficult thing to do would be the expultion of the military units. Also I think it would put to rest most peoples questions as to the realism of culture flipping.
