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.
Didn't Khan say at one point that he put them in the torpedoes, or am I remembering stuff I think I remember?
Yes, Khan originally put them into the torpedoes trying to smuggle them out at some later point. However, he said he had been caught and had to flee.
The question I had was whether Admiral Marcus knew what was inside the torpedoes when he had them transferred to the Enterprise. Both possibilities would make sense.
Come to think of it, one could see the fact that the Admiral had all 72 torpedoes transferred as a strong hint that he knew and planned to have all of them destroyed, together with the Enterprise. For its mission, the Enterprise didn't need that many, did it? It also strikes me as unwise to hand out all of your prototype super torpedoes to one ship if you expect potential trouble to arise (e.g. from the Klingons) in the future. Okay, strategic planning was never Starfleet's strong suit but if I had what I thought were really powerful torpedoes I'd keep some of them for ships guarding important planets and installations.
Maybe that was deliberately kept vague.