It seemed Chekov wasn't aboard the Enterprise during TOS Season One, but the encounter with Khan in ST II suggested otherwise.
Yet "Catspaw" suggests Chekov is new to the ship a few stardates before "Space Seed"... And several stardates after "The Menagerie".
On the other hand, "The Deadly Years" has Chekov indicate understanding of what's so funny about a "corbomite device". If he wasn't there to witness Kirk's original use of the bluff, and his crewmates just brought him up to speed, surely they would also have done so on the issue of Spock hijacking the ship and defying GO7 without consequence.
I think there's plenty of reason to think that death penalties come and go as Starfleet encounters new, dangerous but tempting things mere mortals easily succumb to. Sometimes these are simple utilitarian quarantine measures ("He got contaminated, so it's convenient we have this rule that automatically makes his liquidation not just possible but mandatory"). Sometimes they are there to deter, too ("Few will risk their lives for a potentiality when we slap this approach ban and refuse to explain anything, but if somebody does and gets contaminated, hey, we have the mandate to liquidate him"). These are temporary solutions, though, and eventually Starfleet sends a few Vorgon ships under GO24 to take care of the quarantine problem once and for all. Or then negotiates a peace treaty with the contaminant.
Fundamentally, every Starfleet order contains the potential for death penalty in some form or another: Starfleet employees have the license to kill, and the GO series just regulates how this killing should be conducted.