I do acknowledge that much of the way things are being produced is changing, especially with corporate entities getting involved in farming so much. I don't doubt that this is beginning to mess up the environment. Along with the mass production of anything, there will undoubtedly be pollutants and resources being used can affect things.
There are still however many farmers where I grew up and and elsewhere that do not farm like this. And when it was done like this there were no issues. For example there were no lagoons when I was growing up, which is a big factor on runoff and water pollutants.
Either way, you have to realize that yes fuel is being used means of planting, fertilizing, plowing, and harvesting. Wether or not we give it cattle or people farmers will be producing this. When we stop feeding cattle and put the grain more directly to plants and factories to make food. Great, crop prices dwindle, we just put the last percentage of small farms out of business so the entire industry can be run like the corporations causing the problems in the first place. We are all better off then, aren't we?
I think people are looking at too directly at the problems arising, and looking to fix it in the wrong places. I would argue that instead of putting the stress farming, farmers and livestock production, stop purchasing goods from places like walmart, and mcdonalds, which buy things at the lowest cost possible and produce vast amounts junk that people don't need.
Once people cut down on purchasing beef, poultry, and dairy at places like this and support places like farmers market, local grocery stores, and local eateries maybe, just maybe these corporations would slow down amounts and production causing the problem of needing to produce such sheer amounts of grain just for cattle.