In the prime timeline Spock was willing to risk a great deal for Pike, and it obviously went beyond logic, although it was presented if he was making the logical choices. He felt pretty strongly about Pike. In this timeline he did not have the chance to work with him for years, so it would be weaker, but with all the events that happened some of it would be there. Why wouldn't he meld with him?
He was probably trying to disable Khan with a telepathic attack.
I thought Khan thought that his crew was killed and Spock wanted to reveal it wasn't before driven by his anger he went to cause even more destruction.