I don't think anyone can survive that impact inside a torpedo. If the torpedoes had been fired and actually crashed on Kronos the people inside would have died. That's why I entertained the idea of Admiral Marcus trying to get rid of the evidence that way.
But I'm not sure how far the torpedoes would have gotten without propulsion systems so if they had been fired they might have floated around in space and there would have been the risk of the Enterprise crew investigating the malfunction and discovering the Augments inside.
Which is why Admiral Marcus would have to make sure that the Enterprise gets destroyed by the Klingons. To me, the warp core malfunction pointed in that direction.
But it's simpler to assume the Admiral didn't know about Khan's crew inside the torpedoes.
I don't really remember, but I think Kirk told him, yes.
But I also don't think the revelation that Khan tried to get himself and his people out of Marcus' grasp came as much of a shock to the good admiral.
True. But it would have been interesting if this aspect had been played out more. I felt that 'lack of information' or 'misinformation' was kind of a theme in this movie. There were several pivotal moments in the storyline where this played a role. If Kirk hadn't told Khan the exact number of torpedoes how would he have proceeded? If he had known that his crew was still alive and aboard Enteprise would Khan have crashed the Vengeance on Earth? How would Spock have acted if old Spock hadn't told him whatever it was he told him? And so on.