The makers of Salmon Confidential coincidentally are directly associated with those who are suggesting that the loss of certification due to failing procedure audits is really a punishment for going against the government line so it isn't much of a surprise they predicted it; you might say it's a case of declaring innocence just before charges are laid.
You might also note that the "scientists" quoted in the article referred to in the link-and-run are actually just one person, a statistician named Rick Routledge who again, coincidentally of course, just happens to be directly associated with Morton and the submission of the samples that are at the root of the controversy. In actual fact, the only mention of this conspiracy comes from those who are opposed to farms and there has been absolutely no factual evidence produced to support their claims. In spite of claims of rumors circulating about the controversy, what you really have are some jokers trying to start one.
Atlantic Salmon are used for several reasons. One is that there were domesticated strains available that do much better than wild Pacifics in a farm environment. Pacifics could have eventually been domesticated but there are a few issues arising from doing that. Atlantics and Pacifics belong to different Genera and have some different characteristics, one of which is disease susceptibility and another is ability to interbreed.
If farmed and wild fish have different disease susceptibility there is some reduction of potential for diseases being spread from wild to farm and from farm to wild and less likelihood that one population will become a disease reservoir affecting the other. In spite of the rhetoric, there is an elaborate screening and quarantine process that applied to the importation of all the Atlantic eggs from which farm stocks come and the likelihood of a disease slipping through that process, again in spite of the rhetoric, is very small.
Because the two don't interbreed, the risk of contaminating the wild gene pool with genes selected for hatchery and pen environments is negligible, not the case if large quantities of Pacifics were farmed because some escapes will occur. The other consideration is that in spite of the many attempts over more than 100 years to establish Atlantic populations in B.C. to service the sport and commercial fisheries, none have been successful at establishing breeding populations. The likelihood of escaped farmed Atlantic salmon establishing successful populations to compete with Pacifics has been proven to be very low.