Each and every one of these characters has a legitimate motivation for revenge--Khan for being used by Starfleet, Kirk for the murder of Admiral Pike, Khan for Kirk betraying him... No character steps back from those emotions to show how we should respond...
But Kirk did step back and examine what he was about to do and the morality of such after seeing his officers react negatively to the mission. Much like Picard stepped back from using the virus on the Borg after people like Guinan and Geordi convinced him it was wrong.
Khan was still a terrorist who had a hand in murdering people and Kirk arrived at the correct way to handle the situation.
Sometimes you gotta make hard (perhaps immoral decisions when not at war) when you're in charge.
Archer pirated a ship, killed a clone of Trip when the Earth was threatened. IMO Picard should have sent the virus and taken a chance that the Borg would have been destroyed. Imagine the billions of lives that would have been spared if he did. The Borg had the capacity to wipe out the galaxy.
And Marcus had the right and duty to develop warships as an admiral in Starfleet. He crosses the line though in 'enslaving' Khan and betraying one of his own ships. He's not at war - he just wants to start one.
I agree Starfleet should keep Khan and his guys under wraps. They are just too dangerous for the 23rd century. Perhaps they can be woken up in the 27th