I'd suggest you not use live rock in a tank you are medicating. First off, copper gets absorbed by many things (including calcium based rock) so you probably didn't have the proper dosage for healing the problem. Medication tanks should be bare, with an airstone, heater, and inert things for the fish to hide in ( if needed) like PVC
fittings. Way too many things on live rock that could have died and polluted the water which killed the fish.
Most medications will have a dosage schedule that includes doing partial water changes to combat ammonia buildup. Since the water is new and the fish are probably not eating all that much being sick, the ammonia level shouldn't rise in a properly stocked QT tank for almost a week. ( At east that was the timeframe it took in my warehouse and home tanks.
Lastly, adding fish to an established tank without QTing them or observing them for a period of time is like playing Russian Rhoulette. In the game with a 6 shooter, you have 5 chances to be "right" then BANG, you hit the 6th chamber and it all goes to pieces. That's what happened with your situation, you hit the 6th chamber. Don't blame the tank, it wasn't it's fault
You could say you have been lucky up to this point but proper, successful aquaria are not created by luck but by careful preparation and maintenance of the aquarium's ecosystem. Luck really plays little to no part in a successful aquarium.
I'd just chalk this one up to a learning experience and go from here. Be aware that Velvet ( oodinium) has a long life without a host so I would strongly suggest you leave the tank bare of fish for at least the next 6-8 weeks. Something else to consider is that any invertebrates you have in the tank, like live coral, can house the parasite as well. Since copper is still the best Oodinium medication, and you can't use it on live corals, you should also set up these in a separate tank for a minimum of 6-8 weeks as well.
Unfortunately, even if your solution is to strip down the tank and start it up again new, you should still not use the items in the tank now for that 6-8 week period as they may contaminate the new setup.
I hope some of this helps