Here's my take on the subject:
* Khan plans to steal the pods and put them on the Vengeance, kill Marcus, blow up Section 31, and then steal the Vengeance itself.
* Khan is thwarted by James T. Kirk and falls back to Plan B, retreat to Kronos versus a pre-planned super-transport. He'll there start planning to get back the pods some other means.
* Admiral Marcus decides that he needs to accelerate his plans for a war with the Klingons, deciding to create an expendable crew of pasties to serve as the Lusitania. He chooses the Enterprise after James T. Kirk (noted screw up) volunteers. The fact its crew is mostly only inexperienced goofballs makes it easier.
* Admiral Marcus gives them nonfunctioning torpedoes and intends to follow them to Kronos. Their ship is sabotaged so it will be on the border. Admiral Marcus will then blow the Enterprise up and start their war. The "klingons" will thus be blamed for attacking a defenseless ship.
Khan is irrelevant in Marcus' plans at this point.
* Khan, meanwhile, changes his plan B when Kirk arrives to Plan C and persuades them to help him take down Marcus. Plan C would have involved betraying them once he was in command of the Vengeance.