Well Kawaii has a point, and I was thinking... even if they're the same rank, Leo was directly in charge of the Doma situation, so any others, even some of those at higher rank (if there was one) would have to respect his wishes about his post. He's sort of the head honcho there, while he's there. So Kefka would have to adhere to his words.
And, as Generals, they can all be of different rank. Using America's military system as an example... maybe Kefka was one star and Leo was three?