Regarding when Marcus lost control of Khan, I'm almost positive it was before the movie started. Khan was already running rogue. I doubt the attack on the council/meeting was part of any plan on Marcus' part.
On Enterprise, Khan said he tried to get his people out by placing them in the torpedoes, was found out, and had to escape. His actions having been discovered, he was under the impression his people were then all killed. So he described his subsequent actions (bombing, attack on meeting) as him responding in kind for what was done to him.