This is what I currently think was happening.
Marcus had Khan developing a lot of different weapons for him. The Vengeance
and the torpedoes were just two that we know of. Probably that tiny bomb that blew up the "archives" was another.
Khan had to figure out a crazy plan to outthink Marcus, because he wanted to escape with his people. Khan knew about Marcus's plan to try to start a war with the Klingons, so Khan's plan was to trick Marcus into taking advantage of circumstances to start that war.
Khan did not attack the conference on Marcus's orders. As far as Marcus knew, Khan had gone rogue, tried to kill him, and then escaped to warn the Klingons of Marcus's plan.
Khan had already provided Marcus with a loaded gun, the torpedoes. So, thinking that this was his chance to start the war he wanted, Marcus grabbed that gun, handed it to Kirk, and sent Kirk off to start the war. Rather than just taking Khan out, Marcus probably thought the torpedoes would do some hellacious damage and get the Klingons pissed and start the war. Presumably one torpedo would have been enough for that (imagine each torpedo supposedly having a trunk-full of those explosive pills that blew up the "archives"). Of course, Marcus told Kirk that the drones were just to target Khan individually.
But Khan had tricked and outsmarted Marcus. In case Marcus tried to use those torpedoes in such a manner, Khan had, unbeknownst to Marcus, loaded them up with his people to smuggle them out of Marcus's hands. They couldn't be scanned, so for all we know, perhaps they wouldn't even fire at all. Perhaps Khan had reasoned that Marcus wouldn't bring the Vengeance
out in the open until the war had already started. Ergo, he would give them to a starship not under Marcus's command to fire, assuming he used them at all.
(Did I get it right?)