That would have all sorts of side-effects I think. I'd rather just change things in the DLL to mean that cities are not treated specially for the purpose of invisible units (so an attempt to move into a city attacks the units just as I would if you tried to move onto any other tile that contained enemy units). That would essentially prevent rogues getting into cities in the first place.
Alternatively maybe we need a special action that can only be undertaken by units some new characteristic, to purge criminals from cities (would just bump them out of the city to an adjacent tile). This characteristic could either be an intrinsic property of a unit, or given via a promotion (e.g. - policing promotions)