Right up till the point that he's warned that the new torps are armed at him, Khan could have been following Marcus's plan. Even gunning down the Captains at Daystrom could have been part of the plan, cause it gives Marcus (1) PR and Political capital for the war, (2) takes out anyone that might be a roadblock in his plans.
Once the new torps are in play, Khan gambles on Kirk taking him in and not killing him. When Kirk confirms the number of torps, it confirms Khan's theory that Marcus has sold him out.
Granted, at the end of day, Khan is Khan and he probably had a way or plan to fuck over Marcus when he wanted or needed to, just Marcus threatened Khans family (the other augments) and that was the end of it, Khan went into rage mode.