I dont get what the problem is with the ship being decommissioned so early, even if she was a new ship at the time it was christened as the A.
After the Khitomer battle Starfleet may have decided on the spot to retire the ship for a couple of reasons;
- The Consitution Class, and the Enterprise, represented Starfleet during the time of numerous conflicts with the Klingons, a conflict both sides were trying to put behind them.
- Its participation in the making sure the treaty was signed meant that they wanted to recognize this event and so decommissioned her instead of patch her up and send her off to get squatted by some random phenomena.
To me the events of TUC made the top brass mothball the ship as both a political move as well as a PR stunt. Take her off of active duty and replace her with a new top of the line Excelsior which was nearing completion, a new generation of ship to start the new era of peace and exploration which not only honours the Enterprise and her crew but also the Excelsior too.
That and the hull was compromised. Between the battle damage and what you posted above, I figure those are the reasons the Enterprise-A was decomissioned when it was.
I don't think it was an older ship, more like one of the last ships of an older line.
I know Gene Roddenberry would've preferred that the Enterprise-A was previously the Yorktown but he wasn't in charge of the movies at that point, the Yorktown happened to be in TVH, and I don't see why that ship would've been damaged any worse than any other vessels in the probe's way.
The theory I always lean toward was that Starfleet intended for the yet-to-be-commissioned Enterprise-A to have originally had another name, which was changed at the last minute.