Being in the water pollution field and working with salmon farms all I can say is that the article is misinformation.
First off there are ways to stop the problems of effluent discharge and the sea lice problem by having the farms go inland and not in open ocean pens or open estuary pens. But to do so will take complex wastewater treatment plants just like we treat human waste. They cost many millions of dollars to design, build and operate. If the industry did this then the price of farmed raised anything would be higher than wild fish on the open market. The aqua culture industry does have an inferior product due to such items as food coloring, massive anti biotics which are fed way over the limits that we are allowed to feed cattle in feed yards. Also to rid these fish of sea lice thomaldihide baths are in order for every fish processed.
The claim that there would be less commercial fishing is not a true fact. Yes there would be less commercial salmon fishermen maybe but there are now more commercial fishermen world wide fishing for forage fish to feed not only fish farms but the industrial chicken and pig farms throughout the USA and elsewhere. One serious problem with this is there are no restrictions on commercial forage fish catch here in the USA or anywhere in the world. The United Nations would like to do something about this but most third world countries and the USA will not allow them to do so. The third world countries because they are doing most of the forage fishing the USA and Canada because the Aqua Culture industry is locked in in N. America. One must understand that much of the industry is multi national and that profit in the fish farm industry is not as important as the control of land and sea, it's called land holdings and political power for other more profitable ventures within the countries they are in. Just check out the fish farm industry in S. America and S.E. Asia and see what displacement of coastal villages and violence against those in those countries who dare protest the farms.
I wish fish farms would work but I can see no way that they can. Industrial fish farms will never feed the third world poor even at the price they sell at is way too high because of calories used to grow, process and get to market to calories benefited to human consumption. Fish farms are for the benefit of the the 1st world middle income peoples who have over the last twenty or so years demanded food that is non reginal and out of season. We must stop this life style if we are going to get our calorie out put to human consumption in calories back to a more healthy ratio. It is not just fish farms but all industrial food farming that is the worlds problems. We have been told for years that industrial farming would solve the problems of world hunger it has not.