Originally Posted by Quark
In my opinion, I believe Kirk was referring to the ship as in the name "Enterprise" and her "history" aka lineage of the past starships Enterprise, and now this one. So, while the ship herself--The Enterprise-A--was decommissioned and would no longer be in service, the name "Enterprise" would last forever and a part of her will be within each upcoming flagship.
You may be right.
I personally think it would've been foolish to just put the ship away even though the crew got their orders to stand down. A few repairs after the battle over Khitomer, and the Ent-A would be ready for more adventures under a new captain and crew.
But, dat's just me.