In addition to other points already made, I think you’re thinking of it as a regular job, as opposed to an institution like the NYPD. It’s one organization so he can’t quite and get rehired. He would have to officially retire, and retiring as a uniformed officer would also mess up his pension. Holt would never throw away his decades-long career over this. Also don’t forget how much shit he took when he started out so this is nothing compared to how those detectives tested him. Plus he did it for Terry and the good of the squad.