This is totally not a story about unintended consequences. If you read all three parts (which is a great read), you'll see that the cycle went like this:
Native fish taken out by alweifes
Alewifes taken out by Salmon
Salmon taken out by too few alewives (overfeeding)
Native species recover, because of no alewifes
The original guy did exactly what he set out to do: destroy alewives with salmon and build a fishing economy. That was pretty successful. After that population crashed they eventually discovered that the original fish came back, due to the lack of alewives.
The unintended consequences in this case are positive - marine biologists were able to learn something totally unexpected by doing experiments on a large scale.
The original goal was never to get the native species back; it was to make the lakes back into a commercial fishery. Is the state today "better" because the native species are back? Who knows. Just because things are status quo ante doesn't mean it's better. That population is just as vulnerable to a die off as it used to be.
That's why it's better to read the article instead of skimming it.