I never liked that episode much, so I'm not going to watch it again to see if there's any indication whether Kirk made full disclosure to Starfleet. But if he had, I can't imagine that Khan and his pals were considered to be any kind of military priority or that anyone would think they needed watching, they may have been bastards but they didn't have spaceflight technology, and had no way to recreate even the 21st century technology they were familiar with.
Seriously, if Kirk told Starfleet all about it, and I don't think that's guaranteed, all Starfleet would do is post an advisory about that planet. "Prime Directive in effect, natives known to be hostile and dangerous", that sort of thing.
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