I figured just a time consuming repair in this case. Scotty seemed to have most of the major systems up and running though I'm sure they still needed some attention. My guess is that a lot of the sub-systems were still damaged with a lot of bypassing going on. Which in the end, contributed to the automated system failure. Large components can sometimes be switched out quickly and easily while tearing into the guts of something to make smaller repairs can sometimes be the most tedious. It wouldn't surprise me if part of the miracle Scotty intended amounted to no more than keeping unnecessary systems bypassed while making the jury rigging more reliable.
Would you rather decommission rather then repair and resupply?
Well besides having the shiny new Excelsior class I bet Starfleet Brass is just full of Big Dumbheads(my daughters current favorite insult).