I'm on board with the Yorktown being renamed as Enterprise-A following a refit. As has been pointed out, it's happened canonically with the Sao Paulo, so I am willing to believe that it could happen off-screen with the Enterprise. It could also have been any other Constitution class ship. I simply don't think they would have given him a brand new Constitution, even if they thought he deserved a brand new ship (which he didn't).
That being said, by renaming the Yorktown to Enterprise-A, they're effectively killing the Yorktown. As we know, it later gets new ships as well. There is at least one Yorktown in 2293, because Tuvok's father serves aboard it. Other than the Enterprise and the Yamato, I don't know of any other ships that have letters after their registry (including the Defiant).
Meanwhile, I was flipping through Memory-Alpha to reacquaint myself with the time period, and I was shocked to realize that there is essentially zero time lapse after the events of ST:VI
and the events of ST: Generations
. Both take place in 2293, so it would stand to reason that the Enterpise-A was indeed decomissioned that year to make way for the Enterprise-B.