Ocri asked if we could do it better. So, here's my shot. A little editing would have sufficed.
Kirk et al. have captured Khan on the edge of Klingon space, and the Vengeance intercepts. The confrontation scene plays out as it does, until the Enterprise tries to warp away. At this point, the Vengeance lays some whoop-ass on them and temporarily disables their warp drive (they're already scanning the ship, so they obviously see the warp drive powering up, and also Marcus is expecting deception -- you don't become an Evil Admiral without that distrust). Carol Marcus interrupts the attack, and Scotty intervenes and cuts the Vengeance weapons systems, as we saw. Pretty much everything happens as in the movie, except instead of being between the Earth and Moon, they're in deep space.
Fast forward to Khan taking over the Vengeance, demanding the torpedoes, etc... Kirk et al. get beamed back ("No ship should go down without her captain!"), and just as Khan is about to destroy them, Chekov gets the warp drive back online and they flee to Earth.
Khan transwarps after them, catches up, pummels the ship. Just before the Enterprise is destroyed, the torpedoes explode. Both ships fall out of warp hurdling toward Earth, without power.
At this point, the rest of the movie can take place as shown. Seems pretty much the same, preserves all of the action scenes, without the plot fails. It circumvents the bad physics of the "fall" (except for the ship gravity bit), and the nonsensical idea that no one would even fly by to see why two starfleet vessels were attacking each other. I mean - if two US Navy vessels started shelling each other in New York Harbor, no one would ask 'what's up?'.