This is true, from a certain point of view. In the short-to-medium term, monoculture does allow us to produce more from a given acre of land. In the long run, though, monocultures are more susceptible to disease, pests, or other major environmental shifts, which if we're lucky will only cut growth for a season, but could lead to permanent conditions. For example, the 'Gros Michele' cultivar of banana has now been almost entirely superseded by the 'Cavendish' cultivar.
This is spot on. Our economy does not price externalities well.
Monoculture is efficient because of our methods of working and harvesting. Not because the plants grow better that way. If we had better lighter machinery that could discriminate different types of plants, we wouldn't need monocultures.
On the other hand, there are hints of complacency in the author's arguments as well. To say that gestation crates protect piglets does not end the argument -- it should cause us to ask whether pigs should be bred that are capable of destroying their own young. To say that fossil fuels cause farmland to be more productive does not end the argument either -- it should cause us to ask whether food is too cheap, which is to say, whether all the external costs of food have been adequately priced in. This is not precious high-mindedness, but sober reasoning in light of the fact that catastrophic environmental damage may result from burning fossil fuels, or that serious infectious diseases may result from intensive animal husbandry.
As for farmers being portrayed as helpless, I would say that they largely are. A farmer can hardly avoid the worst practices of the trade if he is to be competitive; which is why it is only reasonable for the worst practices to be prohibited by law, or driven to extinction by public opinion. Certainly law and public opinion can be incredibly ham-fisted, which is why, I suppose, there's value in articles like this.