It is morally repugnant to mistreat animals regardless of the intelligence of the animal and being a scientist has nothing to do with making such a judgment, since it is not a scientific judgment but an ethical one. Thus, the new-found evidence discussed in the article serves only to dramatize something these scientists want because of their philosophical predispositions, not because of their special knowledge as scientists. If the logic suggested in the article were true, the converse might be up for consideration as well (e.g., that we can be cruel to deer because they are so dumb).
Science and advocacy are distinct and should be kept that way. There is nothing wrong with scientists acting as advocates but, when they do so, their views as advocates should normally carry no more weight than do those of others.