As with so many of these things, there's this idea floating around that the factory farms must be "bad" because they are big and wealthy, and that smaller, less efficient farms must be "good" because they are small and poor. Much like with all the other cases, this idea is somewhere between confused and blatant denial of reality.
Money is the unit of caring. The amount of money that you're willing to spend on something is how much you care about having it, as precisely defined by the point at which it's too expensive and you don't care enough to pay that much. The factory farms are big and wealthy because they provide what people care about: an efficiently produced, consistent solution to the problem of what to have for dinner.
If people really cared about their food coming from small, inefficient, "organic" farms then they would pay for what it really costs to produce food in that manner. The fact that people aren't willing to pay for it tells us that they don't actually care as much as they claimed. This is normal: most people will tell you they care deeply about something up until the point when you ask them to open their wallet, and then they remember that they don't care all that much.
It seems to me that what's really wanted here is better factory farms with modest adjustments to reduce pollution, antibiotics use, and improve animal welfare. That's entirely achievable. It won't be achieved by things like this article; it'll be achieved by somebody who sets out to make a better factory farm and builds a business around that.
This is already happening. http://spread.co.jp/en/ plan to have what could be a game-changing approach to vegetable farming up and running in 2017. Whoever gets that system to work well enough at scale seems likely to sweep the 1990s-style farms off the map. It's the exact opposite direction from what the "organic" farmers have been doing: no low-wage labour, no battles over land, no getting caught up in politics.
The next couple of years will be an interesting time for the food markets.