I'd still argue that Starfleet at large was left in the dark, and that Kirk marooned Khan in secret
But if it's in the logs, it's not "secret" (and Kirk's logging it all is part of "Space Seed.")
That's not to say that Starfleet would broadcast that episode to everyone traveling to that system, but I think Kirk was pretty meticulous in his recording of the episode—Kirk may have sympathized with Khan to a degree, but that didn't mean he was willing to jeopardize his own career for him.
Keep in mind that in the "frontier"—be it "final" or American West of the 19th century—the military often was the de facto law in areas without formal civilian justice facilities. So it would be completely normal for a Starship Captain, out in the frontier, to dole out justice in a formal hearing. Starfleet most certainly would have accepted his edict in good faith, as long as he held a proper hearing and documented it as their regulations required.
Orren
Plus, as I said up thread, there is an Augment fear/bigotry in the Federation-- or rather mostly within Starfleet and humanity. The way they might have looked at it is that Kirk saved them some work and headaches (at the time) by marooning him on some backwater planet.
Or to think of it another way: Kahn was a classic leader. He was able to convince people to follow him, even a Starfleet officer (we'll leave out the fact that she just had the hot pants for a piece of living history). Stick Kahn on a penal planet and you're going to have a man that's going to raise up an army against you. Kahn was a cold blooded, smart, charamastic manipulator. Alive in a penal colony he would be dangerous, a risk. Dropped off on some world and forgotten about with only the most barist of necessities to live, he's just a note in a Captain's log.
It is entirely possible that Reliant was sent to the Ceti Alpha system to check up on Kahn and see if he was alive or dead. It was just dumb luck that Terrell and Co. were so bored that they were looking for any excuse to clear the planet for use with Genesis that they beamed down to check out something that most people would have written off as a sensor glitch (Which Chekov first thought).