Kirk isn't protecting his crew when he goes after that SOB. "I watched you murder innocent men and women! I was ordered to end you! You think he was doing it because he wanted to avoid war with the attacker? No. "In the name of Captain Pike..." I shall beat you until my arm falls off.
He isn't when he climbs into the warp core, he only wants to save his crew. Tom Harewood isn't thinking about revenge when he blows up Section 31, he's thinking about his daughter. Khan is trying to save his people for the entire movie and only loses it when he thinks they're dead - although yes, he wanted Marcus dead it certainly wasn't the revenge-at-all-costs we saw in Wrath of Khan (where even the lives of his people were secondary to hurting Kirk)
You think Spock was trying to apprehend Khan? Nope. He was out there to kill him for killing Kirk. That's why Uhura has to stop him "He's our only chance to save Kirk!"
Revenge is on Khan's mind when he kills Marcus.
The end of the movie, Kirk ties it up nicely by saying "we shouldn't try to seek revenge, to act on our initial anger." EDIT:So anger would appear to be the connective tissue between Marcus and Khan and Kirk and Spock. Marcus is motivated by preservation due to his anger that Nero destroyed Vulcan. Khan is angry for being used, Kirk and Spock for someone dying. Acting on the initial anger (re: revenge)
So if anything, the point of the movie is about NOT giving into our urges for revenge - unlike Wrath of Khan, which was Moby Dick in space.