Compare this to the fact that Khan apparently killed nobody!
...Well, yes, technically he presumed he had killed Kirk with the pressure chamber thing. But he didn't really bother to feign surprise when finding Kirk alive and well.
The episode started out with Kirk and his crew idolizing Khan. It really did not end differently. As far as bad guys go, Khan was downright gentlemanly, a man very much to Kirk's liking.
Considering him a "criminal" based on what he did in the past would be pretty thick. He was a head of state, after all - immune to prosecution if anything! What he did after being waken up did not seem to bother Kirk too much, either.
Leaving Khan and company alone on an undeveloped planet with only the basics, no transmitter and no means of leaving to find civilization? Is that mercy, or fundamentally a death sentence?
Neither, I'd think. The planet did not pose any mortal threat to settlers, as far as we were told, and the Earth or Federation colonies we saw in TOS were all of this type anyway: a tiny bunch of people who have severed all ties with their former home and settled down with basic tools and little else. OTOH, dropping Khan off on an alien world is just defusing a bomb, as the endeavor supposedly would consume Khan's ambition and turn his powers to good.