The Despot of Morea was a subject of the Emperor. Just look on any map of the time period. More was a "Sekundogenitur", which means that it was inherited always by the second in the line of the throne. That doesn't mean though it was an independent country. He acted rather independently since there was little central control left, but that can be said about many realms in the medieval world.
I find it strange that Konstantinos is a general in your army and at the same time ruler of Morea, and still you as a player have control over his army, but not over his realm.