those who are high ups at Starfleet Command have served on or commanded their own ships
...So they know the perils of perverse attachment to hardware all too well. That's how it works in the real world, too - if there's an emotional compromise brewing, it's time for some weaning action before it's too late.
It just appears utterly ridiculous
that the feelings of the former Yorktown
CO would enter the picture in any way. He would have been due to leave the ship in X years anyway; getting transferred at a somewhat different date, dictated by higher-ups who don't take requests or listen to complaints, is what you sign up for when you decide that Starfleet is for you.
...Yeah, we could have some sort of an episode where the crew has difficulty adapting when their beloved series-hero CO gets transferred. Like "Chain of Command". But that episode is widely reviled for its portrayal of Riker, Troi and to some degree even Data as disgustingly unprofessional crybabies who bring shame to their organization.