I still find the plan of the Admiral to be a bit murky. If you have those torpedoes, why bother going through the song and dance of giving them to Kirk if you want them to disappear? Why not just quietly make them disappear? They build an entire Starship in secret, getting rid of 72 frozen bodies should be a cakewalk.
That's part of why earlier I thought maybe Khan had tricked him by hiding the bodies in the torpedoes without him knowing it.