If Khan was left alone enough to hide 72 people into torpedoes then why didn't he just wake them up? Surely that would have been a lot simpler.
The explanation that he wanted to sneak them aboard the Vengeance is intriguing. Perhaps he and Marcus agreed to sneak them aboard for some reason before the falling out. Maybe Marcus had some co-conspirators in Starfleet who weren't keen on waking up Khan's crew and Marcus wanted to string Khan along pretending he had snuck them aboard, telling his co-conspirators he had had them killed. Then Khan heard this and did the Section 31 bombing.
I think you'll all agree this explanation is as obvious as the nose in front of your face and required no fanciful fanon from me