Who said Kirk took command when Pike had his accident? Not me. You're agreeing with what I posted. That Kirk doesn't meet Pike until the events of "A Quality of Mercy" in the alternate timeline.It was stated that Kirk took command when Pike had his accident. And that happened in the original timeline.
To quote Kirk in Court Martial:
"But that's not the way it happened."
Kirk met Pike when he was promoted and didn't learn of the accident until The Menagerie.
In the changed timeline he met Kirk as we saw in this episode.