Karl Schroeder had the same reaction I did to the idea of skyscraper farms. But, if you check the bylines, you'll see that I got printed first. Canadian science-fiction author, 0. Me, 1.
One of the most common responses to this idea I get is something like: "forget that, better we learn to live with nature as stewards than apart from it like this." And I admit, the whole "big-box farm" concept is pretty much the definition of separating ourselves from nature. And the idea that we could heal the planet after having wrecked it so thoroughly is tempting. But guess what? We've never, not once, demonstrated the ability to be careful stewards of the Earth.
Anyone who's read Guns, Germs and Steel (or the more recent The World Without Us) understands that the "balance" that pre-contact North American natives lived in with the Earth was less a model of good stewardship, and more the result of having used the Earth to the point of exhaustion their technology allowed: hunting every large mammal to extinction, repeatedly burning forests for better hunting, and a number of other practices. (There's a version of this line of thought that says the First Nations were worse to the environment than we are today, or any number of racist talking points. I hope I don't need to bother stating that simply isn't what I'm saying here.) The old Maya cities are perfect examples of civilizations that overshot the capacity of their natural environment and collapsed.
I proposed in that same Gristmill piece that the basic tenet of environmentalism should be that nature exists independent of human desires or purposes. The prairies don't exist for our benefit -- they were prairies before they were farms, and they'll be prairies when we leave again. This also means that nature doesn't exist to make us feel better about ourselves, or to give us something to do. The best thing we can do with nature is let it go wild. It will recover remarkably quickly if we just leave it alone for a bit. (Making exceptions for places where we've stored truly disgusting stuff like radioactive waste.) So yes, let's replace our horribly destructive, petroleum-dependent methods of farming with something more compact and close the loop -- better that than our current practice of using the Gulf of Mexico as our continental toilet.
But read Karl Schroeder anyway.