On my second viewing, it dawned on me, that once again Khan is taken out by a torpedo. Spock prime must have told NuSpock Khan was done in by an exploding torpedo. I really like that connection, that once again Khan's downfall was a torpedo blowing up his ship.
I came away thinking that Spock Prime told Spock to use Khan's own people against him, since Kirk mentioned it. I may have my timing mixed up, but after Khan and Kirk leave the ship, he immediately calls SP, and then when we cut back to them (after he's done speaking), he is ordering everyone to take the people out of the torpedoes.
I got the impression that Spock came up with the specifics of his plan to take out Harrison/Kahn's ship entirely on his own.