R. Star wrote:
Because Trek hadn't become just "kill the badguy, save the day" yet. Morality, ethics and other things that make you think are what make for a good episode.
Thematically, Khan was discovered having been banished from earth in the Botany Bay (or voluntarily escaped, depending on your narrative). Their punishment was to complete the voyage of the Botany Bay, by reaching "landfall" where they could be given free reign without risking established society. From a story perspective, it's a suitable resolution.