Didn't the engines cut out after the explosion of the torpedoes, which caused the ship to fall to Earth (not to mention that a shockwave in space would be depleted because of the lack of atmosphere, not creating anywhere near the same force, or that the Enterprise falls in manner contradictory to physics)?
They didn't
have engines at that point. Spock says that they couldn't run around the time Kirk decides to team up with Khan and space jump to the ship.
Spock specifically said they hadn't the power to flee. Not being able to run is not the same thing as having no engines with which to stabilize their orbit. Starships have three types of engines: warp, impulse, and thrusters. (Let's ignore for now that thrusters would require chemical propellant, not a quantum source of power.) The first two might be expected as a tool for retreat, but not the third. Their fall was brought about specifically by the loss of power: what instrument was keeping them afloat at the low altitude of 200,000 km up to that point?