He disappeared for five years, to find remains of Krypton... but is it ever mentioned as to what probably happened to Superman when he appeared from the spaceship that crashlanded ? He looked weak and couldn't get up when he reaches for Martha in that scene ?
This version of Superman is portrayed as having a limit to his strength and powers. For example,
lifting the artificial island into space visibly takes all his strength. The combination of this, the kryptonite and the fall back to Earth has the effect of apparently killing him.
Therefore, it is not unreasonable to assume that the impact of his space craft hitting the ground after an apparently uncontrolled atmospheric re-entry would cause a certain amount of injury to him. Obviously, he recovers very quickly.