In my Pax-Persia World game, then i tried to made Native State (and they sure a state - at first they build roads to connect cites) with supposed to slow down colonisation and development of Europe.
Well, then native have several cites under their control - they stop attacking undefended cites. Unless the native unit (like raider in Africa) spawn right near city. In South America was extremely hard to make natives capture even single city. Machu natives didn't want attack. By many many turns those undefended cites was never attacked, even though natives in Bogota build mines and had passage to Andes . But. Then i granted independence to inca's cites - native x-bow spawn near one city and captured it, and several turns late - that happen with another city. I saw something similar, then Inca collapsed - some cites was barbarian and was captured with natives (for some reason barbarian units leaved city for 1 turn and here we are). Look like it was intended?
It also was hard to force them capture cites in USA zone. All those stacks didn't want do it. Only then i bait them with workers - they finally capture cites.
UPD. Also from this game. Portugal was killed before TC events, but respawn with cites, that was never under their control (next turn)