Khan also is the “best “ of the tyrants with Scott and Kirk admiring him, much to Spock’s dismay. So his rep is slightly better than Hitler or Stalin.
Considering the savagery we see that Khan is capable of (Suffocating the crew on the bridge, locking Kirk in McCoy's decompression chamber, torturing Terrell and Chekov, and slaughtering the scientists on Regula I), I'd say it's obvious that Kirk and Scotty were grading on a curve.Remember that there were worse tyrants after Khan, like Li Kwan and Col. Green. Much like Napoleon benefits from comparison with Hitler (lack of genocide helps), Khan's reign looks much better compared to later tyrants.
It also makes me severely doubt that "There were no massacres under his rule" thing.