Super spoilers, obviously:
That's one thought that I had but forgot about. They could create quite a lot of destruction, though they very well may have just jacked the closest vessel and got out of there; it doesn't seem like "he" cared about the Federation other than wanting to get back at intelligence.
Marcus would have known that Khan would be coming back to some extent, and giving him all of his buddies would increase the threat he poses by...a hell of a lot.
I think Marcus really thought Kirk would follow orders now and launch without hesitation (Pike and leading up to it all). Said missiles' original payload very well may have been quite destructive. Knocking out the Klingons' homeworld in addition to Khan would be a win-win.