Are the fish's scales sticking out like a Pine Cone?
An experienced veterinarian can not diagnose an illness without actually examining the fish, so I certainly can't and neither can a fish hatchery. Arbitrarily throwing chemicals and/or medications into a pond can actually cause more damage than good.
It really sounds to me like you have water quality issues. Have you tested the Ammonia levels? It takes a lot more to kill a Goldfish than it does a Koi, and Koi are pretty tough.
Wish I could be more help.
BTW Protozoa are entirely different organisms than bacteria, both being quite common in all water. Sounds like you talked to the janitor at the fish hatchery, based on what they told you.
"Everybody is ignorant, only on different subjects." - Will Rogers