As I understand it, the individual enemy stacks still have one of your cities as a target. Military and diplomatic AI isn't linked so they will continue on to their target regardless of whether or not you are at war. If you exit the game and then load it back up again the AIs forgets what it's targets were so you have a better chance at peace.
I think you're right, because the Mongols/Timurids always go for a certain cit(ies) designated as "horde_target," which are Antioch, Jerusalem, Kiev, etc.

That's why I never make alliance with the Hordes anymore when I have these cities >_>