Hi Sonic,
Rebel diplomats are a common issue after a diplomat obsessed faction, or even any faction with diplomats, has died - when a faction is defeated all of their weaker/moderate forces and agents turn rebel. They often have the habit of turning up on your doorstep begging for trade-rights, ceasefires, maps, settlements, tributes and sometimes even alliances. I think it's a bug really, they should, in my opinion, disband after their faction's destruction for game-play reasons, but they continue living to pester the player with their irritating requests. Sorry.