That's kinda my thought, but then Khan's plan was kinda silly. Did he expect Starfleet to try track him and arrest him? If Kirk had just fired ze missiles at Kronos then Khan would probably be toast. But then Khan's plan makes sense again...because there is no way he could've expected that!
But if Khan put them in the missiles, then what his end plan? Carol seemed interested in the missiles to the point she got on to the Enterprise and said it was because of her father rather than anyone else.
I dunno. I can sorta make sense of it in my head, it could be either.