Have you considered the possibility that the "warheads" in the torpedoes were rigged by Marcus only to prevent someone from tampering with and/or opening them in the first place? This is either because Marcus didn't want the torpedoes to explode either (see below) or because he was hoping that Khan would find the torpedoes, try to open one, only to have it blow up in his face and kill him? Think about that for a moment: Khan helped Marcus redesign the vengeance and the new torpedoes and (if you go by the IDW series) single-handedly destroyed Praxis, arguably spelling eventual doom for the Klingon Empire itself. Marcus' mistake wasn't in waking up Khan, it was in not keeping him under close enough wraps to be able to quickly terminate him when he started to turn. He wouldn't make that mistake twice; the next augment he woke up would have some sort of bomb or other form of kill switch installed that could allow Marcus to terminate him with a simple remote signal. Assuming, of course, that either Marcus or Khan were telling the truth about anything they told Kirk, which I highly doubt. I'm still privately of the belief that this whole fiasco is actually Admiral Marcus' "Bay of Pigs" and that Khan's people were supposed to soft-land on Kronos and take the place over. In that scenario, Khan would be the only one who was meant to open those torpedoes, and therefore, Khan would be the only one who knew the access code to properly open it (he probably set it as the coordinates of Io station, so that any other Section 31 operative would be able to open them safely without the password itself being detectable by, say, Klingon intelligence). Which, again, kind of supports the "Bay of Pigs" theory. If Marcus really knew what was in those torpedo tubes and wanted to dispose of them, he should have shut off their cryo tubes first and THEN given the torpedoes to Enterprise. There's no reason for the augments to still be alive while Enterprise is carrying them, unless the point is for them to also still be alive when they reach Kronos. True. They're potential slaves he can use to help run and/or repair the ship once the mamma eel has more babies.