Khan and the rest of the Augments were responsible for unimaginable death and destruction during the Eugenics Wars. They freely admit they tried to exterminate every human being who didn't measure up to their standards. And now Khan is upset because he has to work for Section 31? Here's what I think about that:
KHAN DESERVES IT.
He is getting exactly what he deserved. He's lucky he's even still alive. Leaving aside for the moment the morality of Section 31's existence or actions, Khan simply deserves to be forced to work for the planet that he previously tried to conquer.
As for the concept of Section 31 holding the rest of the Augments as 'ransom' against Khan? Again: He deserves it. We found out in TOS how much Khan really cares about other people (as evidenced by his treatment of McGivers). The only time Khan ever showed compassion for another living being, Augment or no, was Joachim.