They treated the whole Khan thing way too comic book like. Khan is not the Joker, who is a constant enemy of Batman. Khan is just one of many antagonists, and the crew had to face a lot more problems and adventures.
They confronted V'Ger, the Whale Probe and stopped a Klingon-Federation conspiracy. All that was far more dangerous than Khan ever could haved dreamed of being.
Something about this doesn't quite sit right. V'Ger and the Probe were presented as threats, yes, but ultimately just mysteries to be solved. Neither was outright malevolent.
I suppose it could be interpreted as really meaning most dangerous for the crew, rather than in general. Which would still be debatable. But he was the only one who ever succeeded in actually killing a main character...
Definite yes on the indirect killing of a major character. BUT Khan's potential menace extends beyond the crew. Once he is able to avenge himself upon Kirk, his designs are to once again conquer pretty much everything.