Well, the movie has rogue and "rogue". Part of Marcus' plan to ignite a war with the Klingons would no doubt have involved "Agent Harrison" doing nasty things and then escaping to the Klingon homeworld - perhaps so that Marcus could vector a hothead patsy like Kirk to hit him hard and thus ignite the war, perhaps to cater for some other sort of violent action (but the Kirk option readily presented itself, so there we go).
So everything Khan did until that point could have been on Marcus' direct behest, up to and including strafing the Starfleet top brass Godfather III style and mowing down all of Marcus' opponents while not harming a hair in the Admiral's head. And raiding S31 and then waving at the CCTV camera with the supertransporter bag prominently in his hand would thus have been in Khan's Marcus-dictated itinerary as well: otherwise, how could anybody know that "Harrison" was on the Klingon homeworld?
It would then follow that Marcus also wanted Khan to bomb S31. But it could have been up to Khan to select the method, and he might have done things to the Harewood kid, or then merely found out about her and exploited the situation. The latter is more likely, given the timeline: there would be too little time to create an illness that the parents would accept as incurable.
In what scenario would Marcus not have wanted Khan to bomb S31? How could "Harrison" be exploited to ignite the war if he wasn't seen doing something awfully bad? Sending a "clean" agent to do so, or firing at Klingons for no legal reason, would apparently not be valid methods for Marcus to launch the war.
Timo Saloniemi