No tractor beam could haul the Vengeance in.
Sounds like a situation our characters have to think their way out of. We don't have weapons, we barely have moving power and there's not enough time to warn San Francisco about the danger they're in. What do we have? A crippled, badly damaged Enterprise that can now move and a tractor beam that isn't powerful enough to completely stop the Vengeance on it's own. But we do have those two things working so we can do something with them. What if we get the Enterprise positioned over the Vengeance, lock onto an area of the saucer section with the tractor beam and use every working engine left to push the Vengeance down into the Ocean? The Vengeance doesn't have the power for vertical control, so why not give that idea a shot? Heck, you could use the footage of the Vengeance crashing into the water as it is shown and just cut to a shot of the Enterprise above it being the force that's pushing it down and make a new shot of the Vengeance coming to a dead stop before it hits the city. Khan can still jump out of the ship and you can still have your foot chase.