What a goof. xD
Let’s talk about Khan for a moment.
I don’t pretend to be familiar with the classic version of the character so I speak only from what I’ve seen in this film. Given his back story, I feel there’s not enough exploration of Khan as a truly tragic character. He was made and bred to fight, and yet condemned to death for doing what he did best. He has nothing but his crew, his family - the seventy-two people who followed him into his frozen slumber. Upon waking, his first thought must have been a moment of joy at being reunited with them, until he discovered that not only were they still asleep, but being used to force him into what was essentially slavery. And worse, he was completely and utterly alone.
Savage as he may be, when he shed a tear for his friends, there was no question of its sincerity. He was a dangerous man, but it did not help that he was pushed and provoked and made exponentially worse by his situation. He struck back like a wounded animal, and he killed because when his family was in danger, no one else’s life mattered.
In the end he lost, and yet at the same time won a minor victory for himself - reunited with his family in spirit. The film did not explain what had happened after his capture. They could have executed him - superior as he may be, he is still mortal. They could have imprisoned him, or used him for his knowledge. But the way I see it, it was more likely that they offered him a choice, and seeing that awakening his crew was impossible at this point, he chose to go back to sleep, surrounded by his family.