Civilization – What parts of Civ 5 scale with map size

If you kill quite a number of units of a city state and/or keep trespassing on their territory enough to get your score very very low over an extended period of time, they eventually will be convinced that you are so evil it's not worth considering peaceful coexistence, so they will be in perpetual war with you. You will not be able to buy their friendship and relations will not heal by themselves over time.

Actually that doesn't mean too much, though. If you go near them, they'll attack you, and if you leave cities undefended near them, they'll capture those. Apart from that, they won't hunt you across the map and they won't make others hate you as well. If you just leave them alone now and make their area taboo to your units you can still get along with the other city states just fine.

You might choose to have one perpetual warring city-state next to your army outfitter because city-state units train your troops longer than barbarians do.

If the one remaining civ has 3 city-states that they have conquered, you can liberate them to get your 3 votes. Otherwise you can't get a Diplomatic victory after you undiplomatically crushed all those city-states. =)