Whilst playing SPQR, RTR and the original Vanilla game I noticed that what impacts more on the cultural difference penalties are the Temples. In RTR you can build about twenty temples in a city, so I demolished every temple not belonging to my faction and put one of each kind between the building of more important buildings. This, though, does not work in RSII.
Shame, the only thing to do is to exterminate the popluation.