For one thing, its considered bad luck to rename a ship
Umm, no. It's a time-honored custom to rename ships, especially warships that change ownership. You just have to do a silly little ceremony to appease the gods of the sea, if you're into that stuff.
It does just seem that the E-A was about giving Kirk what they thought he wanted.
what he deserved. They did give him a ship of somewhat aged type that wasn't working properly and got decommissioned half a decade later. And then they gave him an assured-failure mission to perform with her, in ST5:TFF. And after he succeeded against odds, they gave him another assured-failure mission, in ST:TUC, hoping that he'd die and/or ignite a war. And then it turned out that the ship would be decommissioned, after barely half a decade of service.
Those are the apparent facts; whether they should be interpreted as Starfleet really liking Kirk or Starfleet really hating Kirk is for everybody to personally decide...