To me, the most suprising "twist" of the movie was that they almost turned Khan into some kind of anti-hero.
From a certain POV he had legitimate reasons for the London bombing and the attack on Starfleet headquarters. I would also point out that Khan had fully cooperated with Kirk and his crew... up until the moment when Kirk ordered Scotty to shoot him. That's the moment when Khan turned on Kirk. Khan probably figured that Kirk must be another Starfleet scumbag just like Admiral Marcus was.