The entire thing with the torpedoes is a bit convoluted, but within the logic of the movie, he's what I (at least) thought was happening:
-- Khan was in charge of developing the torpedoes.
-- Khan somehow had access to his people and believed he could smuggle them out inside the torpedoes.
-- At the right time, he would board the Vengeance when the torpedoes were delivered (the ship I'd imagine they were first designed for) and secretly thaw his people. They would take over the Vengeance and be on their merry way.
-- Marcus found out about the people in the torpedoes. Khan fled, and the events that we see in the movie unfold.
-- Marcus decides the best way to carry out his plan with things as they are now is to get rid of Khan and his people by giving the torpedoes to the Enterprise and send them on the mission to Kronos that he hopes will start a war.
-- Even without armed warheads, the torpedoes are almost certainly fueled (maybe by Section 31 before giving them to the Enterprise) and maybe warheads were even added.
-- In any case, even if they were all fired as duds or just the detonators exploded, it would still be an attack on the Klingon home world, and all hell would break loose.
The thing that's rather silly about the plan, though, is the need to fire all 72 torpedoes. Even if Kirk intended to use them, he could've decided using them all was too risky for starting a war, so he could've located Khan and fired only one or two at his position, which should've been enough.
Anyway, that's my best attempt at all this.
And its not a bad summary given what we know in my view, but there are still a few issues:
- Why would Marcus keep Khan's crew anywhere near Khan?
- Giving the torpedoes to Kirk (a known loose canon) and in such quantity, especially with the requirement they not examine them, was asking for trouble. Why take that risk when he could have just removed Khan's crew and not raised suspicion, comment or resignations?
- Of course there is unlikely to be room for fuel or a warhead when what looked like well over half the internal volume was taken up with something that is not supposed to be there.
- Even if armed and fuelled, what was so special about these torpedoes that standard models couldn't do given that Kirk managed to get a small ship all the way to the Klingon home-world?
By the way, I must have missed something, why would Section 31 be looking for Khan in the first place? Wasn't Spock Prime supposed to be keeping quiet about his future knowledge and even if "forced" to give them something, why Khan? He was discovered by accident last time wasn't he? Wouldn't Spock prefer to leave him be and tell them about the planet smasher or something?