... but what if, in-universe, the plan was always to launch the Enterprise E anyway, and keep the former Enterprise in service under a different name? Maybe they intended to launch the Sovereign Enterprise the following year, regardless of whether her predecessor was destroyed. What if the changes made to the bridge module in "Generations" (vs the one seen in the series) were because the Enterprise had been recently refitted in preparation for it's rebranding/being handed over to a new crew, while Picard and the rest (and the Enterprise name itself, of course) were going to migrate to a more updated vessel. Under this hypothesis, the 'death' of 1701-D was an unfortunate coincidence, but not a crippling difference to the plan except fo the loss of a Galaxy from the fleet. Because maybe the new Enterprise was already on the starting blocks undergoing final tests, and the crew were readying themselves to move over to the Sovereign Enterprise anyway. The only crew who lost out in this scenario are obviously the ones who might have been intended to take over the former Enterprise-D.
You have an interesting theory there; however, I'm not sure it applies to the Enterprise-D. I just don't think it would have been renamed, and I certainly don't think that that Sovereign class ship would have been an Enterprise had the previous ship not been destroyed. Even "All Good Things" makes it clear that the Ent-D, while considered an old ship in the anti-time future, was still named the same and had been given significant upgrades in its technology over time.
However, I think your theory has merit for a previous Enterprise, namely the Enterprise-A. Here's what I theorize:
In Star Trek III, Admiral Morrow states that the original Enterprise was going to be decommissioned, and that ships like the Excelsior were the future. I believe at this early point there were plans to build a new Excelsior-class Enterprise and have it be the Enterprise-A, which was why Starfleet wanted the former ship mothballed.
However, because of Kirk's actions in STIV, Starfleet decided to give Kirk an "intermediate" Enterprise (since construction hadn't been started on the new ship yet), and let him fly it around for a few years until the Enterprise-B was completed. This would explain why the ship was decommissioned at the end of STVI.
But what happened to the Enterprise-A? While there's no canon confirmation of this, there's every indication that the Enterprise-A was a brand-new ship. So why build a new Constitution class ship just to decommission it a few years later? Well, because there were already plans to build the Excelsior-class Enterprise, the A needed to be out of the picture by the time the new ship was commissioned. It's my personal opinion that the Enterprise-A was then recommissioned with a different name, and lived out its normal lifespan as another ship.
There's also speculation that the Enterprise-A was in fact an older ship that had been renamed the Enterprise. If that's the case, then I would surmise that after those few years as the Enterprise, it was given back its original name, whatever that was.