McGarrett may not have been guilty of killing the Gov, but he did commit several crimes he should have to answer for. Escaping custody, assault on a police officer, theft (the uniform), grand theft auto, etc.
The man should have plenty of jail time ahead of him.
Thats like saying Spock should have been dishonorably discharged and jailed for the crimes he committed in "the Menagerie". Not gonna happen!!!
Slap on the wrist and a return to the status quo!!!!