Gifts and alliances can do the trick...
I will often reduce an AI civ to a punching bag with just a couple of island towns / cities. They are, of course, furious. As time goes by, especially if I can achieve a branch tech lead, gifting them semi-obsolete techs, any excess of the newly appeared strategic resources, and any excess (monopoly) luxuries, I can almost alway swing them back to polite.