I see two options: either he wanted to use the Augments on the Klingons and weaken them before invading, or he thought of killing two birds with one stone: killing Khan with the very torpedoes containing his people, and bombard Qo'Nos and start a war, conveniently wiping out the only witnesses (the Enterprise).
Probably not the former, given that the warheads were still active. The problem I have with the latter is that it just seems like a bizarre and frankly roundabout way of cleaning up his mess. The guy's involved with Section 31 and has the clout to build and captain a ship like the Vengeance. If he wanted the Augments gone, why not just dump them in an incinerator somewhere and hide the paperwork?
When it was revealed that Marcus sabotaged the warp core and stranded the Enterprise on purpose, my first thought was that he intended the Klingons to find what appeared to be a Starfleet ship smuggling supersoldiers into their space, and that that
would be the pretext for war. But then it turned out that the torpedoes were live and Marcus did want them to be fired on Kronos, so...
The frustrating part about all of the Khan/Augment stuff is how close it comes to making sense, and yet...not...quite. I feel like they could have given that element another pass and really polished it up. Alas.