Star Trek: Khan - Ruling in Hell IDW Publishing October 2010 – January 2011
From issue 1
Kirk states his concerns that Khan could easily escape a re-education facility or Starbase. His preference was having Khan focused on this new world.
https://memory-alpha.fandom.com/wiki/Star_Trek:_Khan_-_Ruling_in_Hell
Additional comment that this mercy is in character for Kirk as also seen in the episode "By Any Other Name". The villains in this were lovecraftian aliens from the Andromeda galaxy that killed a member of his crew!
Transcript from http://www.chakoteya.net/StarTrek/50.htm
ROJAN: We have a duty, our mission. We've got to accomplish any way we can.
KIRK: Your mission is to find new worlds for your people to live in. You can still do that. We can bring this problem to the Federation. There are many planets in this galaxy that can be inhabited.
ROJAN: You would really do that? You would extend welcome to invaders?
KIRK: No. But we would welcome friends.
SPOCK: Rojan, you are only a link in a chain, following an order given three hundred years ago. This is an opportunity for you to establish a destiny of your own.
ROJAN: Perhaps. Perhaps it could be done.
SPOCK: A robot ship could be sent to Kelva with the Federation proposal.
