"You could have done that at any time in the last several weeks." Between the regular letting of his blood, and Kirk's own adamant declaration that John Harrison was going to stand trial-- eventually-- for his crimes, it seems unlikely that even Kirk could get away with making him disappear, not unless he was willing to produce a corpse and claim that Khan had been killed during some escape attempt.

"It would be far more efficient to kill me. Fewer questions, although I imagine there will still be an investigation into the sudden disappearance of Earth's most wanted terrorist. Or are you attempting to get your crew used to lying to the Federation for you?"