You know who I think the real villain of The Wrath of Khan is?
Carol Marcus.
She used military resources to create and test a device that could obviously be used as a weapon (it was even supposed to be loaded into a torpedo) that was not stored securely enough. And she claimed it was intended only for peaceful uses.
On top of that, she had the Reliant explore the Ceti Alpha system and there had to be Starfleet records that the system was inhabited even if the specific planet wasn't, making testing the device an inherent risk. Expecting me to believe that there are no lifeless bodies in uninhabited systems is ridiculous.
(Why no one noticed a planet was missing in the Ceti Alpha system is a question I can't answer.)
She offered Khan a chance to escape his planet, get control of a powerful ship and steal a weapon of mass destruction.
Also, on a more minor note, she didn't tell David that his father existed and made him hate Starfleet.
My head canon for what happened to Ceti Alpha and Khan is Kirk submitted his captain's log and Star Fleet classified it out of fear of an unfinished rivalry built up around the conclusion of the Eugenics Wars. The Reliant had no ability to access that information and only had the same stale info on Ceti Alpha that Kirk had a decade prior.
The real villain is the Federation for funding what could easily be a weapon AND hiding details of an exiled war criminal. There are so many skeletons in the Federation closet that with enough radiation it would be a Halloween episode if Section 31 ever became a show.
Counterpoint: Khan tried to take over the Enterprise and kill Kirk with basically no provocation. Kirk even found out he was a 20th century dictator and all he did was confine him to his quarters. He didn't even put him in the brig. It sucks that Ceti Alpha IV became inhospitable to life, but the fact that he let him live freely on a planet instead of spending his life in a Federation prison was a pretty sweet deal.
Kirk's only crime was not coming back to check on Khan or sending anyone else to check on him either, although that could totally be down to Starfleet command. Although even if SFC didn't send anyone, you would think Kirk would want to make sure his former crewmember was doing all right.
Yeah, it definitely would have been consistent with Kirk's character to want to check in. But honestly, if he was like, "You tried to blow up the ship and kill my entire crew. I'm giving you some supplies and then you're on your own," that would have been more than fair. Now, if he knew Ceti Alpha VI blew up and was like, "meh, not my problem," that would be one thing, but it seems like everyone in the Federation was caught off guard there.