First, you had no way of knowing why the fish wasn't eating. The fish could of had flukes, intestinal worms, a bacteria infection, a parasite in its mouth, a damaged mouth, or possibly a reaction to the medication that it was given along the way from being collected. All of these things could have caused the fish to stop eating and a fresh water dip or bath wouldn't have helped with most of those things. Bottom line, he probably should have made sure that the fish was eating and doing good before he purchased it, but nowadays people just buy fish as soon as they arrive.
Most fish can take fresh water dips just fine, others stress out very heavily and can go into shock and die. You need to be very careful when doing one. In some case a fish that is doing bad a fresh water dip may help, but you'll find in most case it just stress the fish out more and bring about the fish dying faster.
As for the link that you posted, well first off there are different types of flukes, with different type of methods of breeding. You'll also see that most of the method talked about in the article are about containing the flukes and not eliminating them. As for hypo killing them completely, well I suggest you read up on threads on RC, where people have been combating flukes, and you'll see that hypo doesn't get rid of them from your tank, as once you're done with the treatment they come right back.
Once they're in your tank it's very hard to get rid of them and the the only really method to eliminate them is to treat all your fish separately and then leave the MT fallow. Now reef tanks, with the corals feeding on things, inverts, including shrimp and crabs, and filter shock can in time possibly eliminate or control them. But you should also QT all your fish before you place them into your tank in the first place, and treat any fish that you suspect of having problems. Then again it's very possible that fish you have right now may have flukes and you just don't know until they die for no reason.