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.
Do you remember where or who stated that "Kirk took command when Pike had his accident"? After Spock's mind-meld with Pike he assumed that someone else would captain the Enterprise because of Pike's accident. Spock would have no way to know that in actual TOS that Jim Kirk would meet Pike during Pike's promotion before the accident or that Kirk didn't take command due to Pike's accident.
If it were to go down like in TOS then SNW Kirk should somehow avoid meeting Pike until he gets a promotion and then they can have interaction. So maybe SNW Pike gets promoted to fleet captain in S2 to jump start the interaction.
From "A Quality of Mercy"
SPOCK: The accident in question was six months ago. In this timeline, there were no cadets at the reactor incident to save. No one was even hurt.
PIKE: I need your help, Spock. I was sent forward to this moment in time for a reason. We have to figure out why.
SPOCK: I would posit that in this present, you were never injured in the training accident, thus you remained captain of the Enterprise, putting you in charge at a crucial moment in the ship's existence.
PIKE: A moment where the whole future hangs in the balance.
SPOCK: All we can surmise is that, in the prime future, some other captain of the Enterprise must have commanded it differently. Thus, it is imperative you do not change what you would normally do on the ship.
PIKE: I thought we were trying to avoid a terrible future.
SPOCK: We are trying to discover why this future is, in the estimation of your older self, worse...
and from "The Menagerie"
MENDEZ: You ever met Chris Pike?
KIRK: When he was promoted to Fleet Captain.
MENDEZ: About your age. Big, handsome man, vital, active.
KIRK: I took over the Enterprise from him. Spock served with him for several years.
SPOCK: Eleven years, four months, five days.
MCCOY: What's his problem, Commodore?
MENDEZ: Inspection tour of a cadet vessel. Old Class J starship. One of the baffle plates ruptured.
MCCOY: The delta rays?
MENDEZ: He went in bringing out all those kids that were still alive. Just wanted you gentlemen to be prepared.