I don't think that it was meant to show that Kirk earnt his captaincy by being one of the few captains left alive. He only really got his captaincy back by being a suitable patsy for Admiral Marcus.
I think the captaincy was supposed to be earnt by his actions in the entire movie.
As a Star Trek fan I thought the sudden captaincy at the end of ST09 was very surprising but thought they were trying to appeal to a younger audience.
I felt actually Kirk had earned his captaincy a bit at the beginning of STID by not letting a civilisation die unnecessarily, and not having any deaths in his crew for 6 months. I thought them taking the Enterprise off him was a bit petty of Starfleet. If they were actually concerned about the Prime Directive they should have courtmartialled him