Hmm. Why would Marcus have ordered exactly 72 of the long range torpedoes? If he ordered a different number, and Khan only modified the significant 72, then knowing that Sulu is aiming 72 at him should be indication of nothing much.
Khan didn't know the number until Spock told him on Kronos. When Khan realized that Enterprise had some long-range torpedoes, he probably started to wonder if Marcus was panicking and trying to destroy all evidence of the augments
Also, the idea seems to be to let Kirk fire the shots, after which Kirk dies in the hands of the Klingons. Firing the shots from the Vengeance would be a bit less clever, as Marcus apparently wants to expend a Starfleet vessel so that it looks like the Klingons are the bad guys, and he certainly wouldn't want to expend his best warship!
I think Marcus just took the opportunity presented by Khan fleeing to Kronos to accelerate his plan, plus dispose of the torpedoes. I can't imagine the original plan was to sacrifice Vengeance attacking the Klingons.