I've read a similar claim in The Omnivore's Dilemma by Michael Pollan. According to Pollan, most fertilizer is manufactured with petroleum-based energy, so our agriculture is driven by fossil fuel consumption; ie natural gas -> fertilizers -> corn. This is not necessarily a vegan agenda; Pollan says we should move to solar-based agriculture by feeding animals grass instead of corn, which should incidentally make the animals tastier and more nutritious.

I haven't found any evidence refuting Cowspiracy's claims, unfortunately, which has cornered me into eating vegan for going on two weeks now.

If healthy vegan food were subsidized as it should be, most of the issues with limited food/dish selection would probably be addressed in no time.