The funny thing is they were far more fucked with Marcus at the helm than they were facing Khan, because at least with Khan they were already well aware of his weaknesses. Marcus only gave a shit about his position and career, Khan at least cared about the lives of his fellow freaks.
Kirk's response to the no-win scenario was to desperately and selflessly plead for the life of his crew. "Prayer, Mr Saavik - the Klingon's don't take prisoners" - not so smug are you now, eh Kirk? This Kirk saved Earth as a fucking cadet, so of course in this movie he had to get taken down a notch or ten by facing a true Kobayashi Maru where he was absolutely powerless. And until his final sacrifice he escaped each time by luck or the help of others just as Pike said - Khan bails him out on Kronos, Scotty saves them all from the Vengeance, Kirk is then forced to trade one enemy for another (giving Khan the most powerful ship in the fleet, good one Jim!), and ultimately his only option left to save anyone cost him his life. Not Kirk's best day.
Kirk had to choose Khan over Marcus though, and not just for the chance to save his crew. A war with the Klingons was a bigger threat than Khan and his buddies. It's unfortunate I guess that Khan was the lesser threat in the movie - but cool that Khan was the only one able to defeat that threat.
Did you catch that Spock's quip about the "enemy of my enemy" quote was dead on? Heh.
I'm glad they didn't try to come up with some roundabout way to make it about Kirk Vs Khan 20 years too early. Oddly, it was Spock who wound up being the one seeking personal vengeance.
Probably my only real gripe is it was way too obvious how Khan would go down. He had already figured out option B (blow up the ship, recover the popsicles) so why even take the risk? Well, shit, I guess its in character - because just blowing up the Enterprise would have been too easy. His ego doesn't let him just win that way as has been well established. But come on, he knew he couldn't just scan the torpedoes because he made the damn things.
Oh, and Khan vs the Klingons was fucking awesome and will probably be the highlight of the movie when I watch it again down the road.