You seem to think that carrier command required existing pilots to be groomed to be captains. That is not the case. The Navy used officers who had already proven themselves in command on other ships, but they needed to attend flight school before they could command a carrier. Halsey was already a captain when he got his wings in the mid thirties. Afterwards, I wouldn't be surprised if he never flew again. Most of the prewar carrier captains were exactly the same.
Potential future carrier commanders would have been identified by Nimitz far in advance. If he wanted to give someone the job, but he hadn't had flight experience, it would have been easy to tell the person, "Get your ass to Pensacola and get your wings." There was more than enough time for a prospective captain to go out there and do so. However, I don't know enough about the carrier captains during the war to confirm that this was ever done.
It may even be that the requirement wasn't followed during the war. I don't think Spruance or Fletcher ever qualified as pilots, but I think they were admirals in charge of carrier task forces, and not captains of the ships themselves. Can't remember the details right now.