I've always believed that Pike's accident with the cadets that crippled him came after he had already been promoted from the Enterprise. I'm having a hard time seeing how he could still be captain of the ship in Kirk's time. If it wasn't Kirk in command in that period, it should have been someone else besides Pike, too.
Because the story calls for history to be altered 22 YEARS in the past, so anything that happened in the normal timeline didn't necessarily happen in the altered one, e.g. Pike's promotion or anything else you want to change for the sake of the story.