To me, that says more about Starfleet than it does Kirk and his friends.
Which gives Starfleet all the more reason to chastise the heroes!
That the vessel was a prototype carrying high expectations only makes what happened worse, because the Federation wasn't able to test their new technology as planned.
How so? Supposedly, yanking out a few chips would be trivially reversible, and the ship would be back at transwarp testing in no time flat.
Whether those tests were a splendid success or an embarrassing failure, we don't know. But we never were told that Scotty would have broken the ship for good.