Pauly and Jacquet object to the proposed certification of the fishery because much of the catch goes to feed farmed fish and land livestock - a process which is usually seen as fairly wasteful given that several pounds of fish are needed for each pound of livestock or farmed fish produced. And it's not as if anchovies are inedible otherwise. The domestication of ruminants was extremely useful for early agricultural humans - regardless of the pounds in-pounds out comparisons - because humans just can't digest pounds and pounds of grass, and ruminants can. So they convert, in a sense, inedible things into usable protein. Anchovies, on the other hand, are quite edible, and full of protein. As the authors point out, Peru has a serious problem with child malnutrition and it makes little sense to export a source of good protein when people are starving. Protein isn't just for building nice biceps, since protein-deficient children usually end up with low IQs in addition to physical ailments.
The problem with MSC, the authors point out, is perhaps not that anchovies are overfished (it appears that they aren't) or that fishing methods are harming the environment, but that the wasteful practice of feeding farmed fish (or livestock) with fishmeal is not taken into account. This is yet another problem with the MSC standards. It increasingly appears that these standards simply aren't tough enough to ensure that certified fisheries are held to the highest standards. It seems to me that any fishery that can make a somewhat plausible argument that it meets the standards gets to use the label. The certifiers are working on behalf of the fishers - not the ocean. Since MSC is supposedly about protecting marine species first and foremost, why does it seem that MSC ignores so many of these kind of issues? MSC certification cannot be considered credible if it is so easily obtained, with no thought given to the broader impacts of certification. More here.