I've seen a number of threads discussing how to avoid a very serious diplomatic penalty from Civilization V's AI when engaging in war. We talked about a couple on the 126th episode of PolyCast, and a brief search revealed yet another. I'm sure this is not an exhaustive list of the threads, and certainly not individual posts within others, that in part is getting at: "how do we completely destroy, or at least deal the final blow, to a civilization without getting the 'Warmonger' diplomatic penalty"? It can have severe repercussions if even one AI player takes this position towards you, for even they are not a threat individually others are likely to follow leading to denunciation and further conflict which may very well pose a problem in the near-to-distant future.
The discussions I have come across, and have had, on this matter inevitably recommending generally to leave the AI with any one city standing: let an AI, 'proper' or City State, deal the final blow if they wish... avoid that "warmonger" menace label, or at least increasing the AI disposition towards it, on yourself. In clarification, you can indeed be labeled a "warmonger" even if you do not take out the out an AI's final city, but it seems to be all but guaranteed that disposition will emerge -- or increase in propagation and severity -- if you do. Anything to lessen its presence, and impact, is welcome.
It was during setting up a new game in the past week that another alternative struck me, one that I not seen mentioned before, leading me to at last put it to a short-term test this evening. If I've missed any earlier mention(s), this thread will consolidate this approach into a dedicated thread at least.
This is a sequential two-step process, where one needs to set the following in setup or what you do in-game won't yield the desired result. This can work for Single Player, as well as Multiplayer where either AI are placed at the outset or after one or more drops an AI takes a human player's place.
1. Using the "Advanced Setup" window, under 'Advanced Game Options' check the "Complete Kills" button. As described when hovering over this point: [i]n order to be eliminated from the game, a player must have all of his Cities AND Units destroyed.
2a. While engaged in war in-game, find a unit of of your AI combatant and purposefully do not destroy it... ideally not a Settler. (If the unit is in danger of being killed by another player, take as reasonable steps you can to isolate/protect it.)
2b. Take out your AI combatant's last city. Though the AI has no more cities, they have not been eliminated from the game thanks to their surviving unit (or units).
An interesting aside: in getting peace with this combatant AI the same turn that I took out their final city, I was able to get all the gold in their treasury and -- strangely -- the gold-per-turn that they were still generating as part of our treaty. (I substituted "Open Borders" for 1gpt for some reason. ) Through a game save re-load, I was able to secure the same treaty terms the turn following too.
First, I acknowledge it may not always be easy or quick to find a unit to "save" the AI your fighting. If they are to the point of being unitless, in the vicinity of their territory anyway, you would have to wait for them to generate one and move it out their city. Unless you're worried about another player taking that city in the interim, either to keep or burn, I'd withdraw and wait for the AI make and send out such a unit.
Second, if the AI has a Settler as their only/another unit, they will settle if and when they can so you may want or even have to repeat this process, depending upon their rebuilding success.
Third, I haven't tested this with City States specifically yet, but I expect it would work the same.