Theory 1: Khan was a 'scape goat. Someone unconnected to the fleet, running around causing trouble, and given Marcus the motive he needs to roll out the BFG Vengeance.
Theory 2: Marcu's was (A) an idiot and thought he could control Khan. (B) Was going to use Khan and his augment crew as his own personal army.
Exactly, Vengeance was already underway, Marcus wanted an uncivilised view of warfare, weaponry, tactics and ideas to basically put every under handed advantage possibly into his ship and think of every contingency should it be needed.
Proofing, not building. And I suspect had Khan not escaped, Marcus would have found another way to incite war, and simply dispose of Khan and his men immediately after.
This why I keep thinking the Vengeance is a pre existing or publicly known next-gen class of ship that was jacked up on steroids to the point that Kirk and Co. didn't recognize her right off the bat. The Abrams' universe equivalent of the Excelsior project--only hijacked by a madman and his pet augment.