It was an error in the writing of the episode in some ways, but not the biggest one - worse story points include Kirk giving unknown persons full access to the ships computer to the point they can work out how to work it, McGuivers helping Khan after he smacked her about and Khan wanting her after she helped Kirk and Spock retake the ship.
But what did you want him to do, Kirk killed Mitchell as a last resort, he didnt want to do it, and we know he offered to help the Romulans after he crippled their Bird of Prey - Kirk was a man who would kill when he had to but would offer a chance to live when he could.
The biggest problem is why no one stopped off every so often to see how a potential threat was doing, by WOK Starfleet seemed to forget they were in that system (and hadnt noticed a missing planet), any Starfleet ship surveying that system should have had orders to scan the planet.
In the real world if we found a group of mass murdering dictators in a bunker in cryo sleep and didnt have the option of keeping them in the freezer are we really saying we wouldnt take them back for trial and instead dump them on an island somewhere?
Seems a little short sighted.
"In the real world" has no place in this discussion. It's Star Trek. It's fiction. Reality doesn't count.