you don't have to kill the sovereign - you can also demand his surrender, which will destroy all remaining cities and outposts and make him your vassal. he basically becomes a champion of your civ and keeps all his ablities and all the stuff he has, though he gets a negative promotion "broken spirit" that reduces his accuracy and spell mastery by 25%. this is usually the best way to end a war of annihilation against an AI, since this also conveniently gives you the faction prestige of the sovereign (basically his level divided by two - just like your own sov). and it gives you access to his sovereign profession (like for example  if you make lord relias a vassal, you get his "adventurer" perk that allows you to recruit champions for free, or if Verga becomes your vassal, unit wages are cut in half sine you inherit his Warlord perk) 

I always set Surrender Threshold to Often (which basically means they will consider surrender if you are more than twice (or is it three times?) their faction power and they have few or no cities left).  If they are "too busy to talk" you can still talk to them if there is at least one sovereign you can talk to which you can scroll to the "busy" one.

I usually make them surrender rather then kill them. Even if they don't have good traits you can use them as a governor; and sometimes they have good gear.

Or if your evil there is always steal spirt. A Master Death/Life/Fire mage is fun.

Has anyone run into the other situation in my OP, that of three cities with the same name founded by the same faction? The other strange part of the game is that two of the factions were founding cities, expanding etc., and the other two founded a single city and a few outposts but no more cities.