http://en.wikipedia.org/wiki/Monoculture of annual crops already have a lot of problems: soil erosion, the "pesticide treadmill" effect, loss of soil nutrients, etc.
Modern industrial agriculture needs A LOT of inputs - synthetic fertilizer, pesticides, and water. As long as the real costs are hidden (subsidies, not taking into account the cost to the environment, cheap fuel prices for creating synthetic fertilizer, etc.), then industrial ag will continue to be the norm. Water wars are already being waged - the largest consumer of water is agriculture. Practices are starting to change among many farmers, but certainly not the huge industrial sized operations.
However, discussion of crops isn't exactly in the scope of this thread?
As for confined animal feeding operations (CAFOs): CAFOs =/= large-scale cattle operations. http://en.wikipedia.org/wiki/Confined_animal_feeding_operation.