He wanted a war and what better way then do do this attack and then rope the Klingons into it with the Enterprise.
I guess the only better way would be to frame the
Klingons for some atrocity. But supposedly the real Klingons were already doing atrocities left and right, with the Starfleet doves still purring happily; adding one in downtown London might not carry enough weight. Plus, mixing Klingons into all this would be a bit too unpredictable in practice, while not being sufficiently unpredictable and threatening in appearance.
But bomb S31 so that top brass (including the doves) gets summoned, then eliminate that top brass save for a sucker who gets his motivation from the deaths, and you have a controllable chain of events...
Yes he got injured in that attack but Khan was skillful enough to kill everyone but him.
Indeed, Khan chose weapons that
could wound, when he would certainly have had access to ones that would have guaranteed a kill. Perhaps Marcus' wounding was a nasty extra element not agreed upon - and also something that Marcus would accept as the nastiest bit of rebellion Khan would dare pull off when Marcus still had his crew by the short and sensitives. Essentially, Marcus would feel more confident and relaxed now that Khan had made him bleed!
It was a setup and that's my opinion. Also the transwarp transporter. Starfleet confisicated that from Scotty and Section 31 turned it into a portable device. Khan had to get his hands on that device and Marcus let him.
...For all we know, the thing doesn't even work (which would be nice for future plots), and Khan flew to Qo'noS by conventional means!
This is just all my personal opinion, the movie doesn't say either way if they had planned this together or not..
The one major argument for the preplanning theory is that neither of the villains would have come as close to their personal goal as they did unless they indeed cooperated. But it's certainly open to many interpretations.
Timo Saloniemi