Well the first time I used process_cq is to get rid of CTD, and the citry on which I used it did not have any pacification building, so I guess the cheat should not have eneterfeered with other cities.
As to the other cities that have pacification building for ages (or in some cases governor's villa repairing for ages) process_cq will not work (it will complete all the buildings AFTER the pacification, but not the pacification itself).
Also I noticed that too often I would get no pacification, but instead asked to repair their native government (frequently there are two copies that need to be reapired), some of these native governments repair just fine, some take ages - just as pacification. I am not sure if this is normal either...