There is a catch-22 with farming. More antibiotics/immunizations helps protect the livestock, decreases incidence of broad-spectrum infections, and having bigger productions means more inspections, etc. Smaller farms won't feed the same massive amount of people as we have now, but they will isolate the livestock more to (hopefully) avoid the infections. On the other hand.. all of those antibiotics and hormones are clearly affecting the food and the people consuming it, and it's allowing room for conditions that would be hazardous to the animals otherwise (lots of anything in a small space is bad health news), and the quality of food is less than with small local farming--and so is the price.
I'm not exactly sure what the right answers are.. but I've been doing a lot of thinking on the issue. I know there is a morality I do tie with food, that I've only recently even had time in my life to think about, and going about it in the best way possible is something I've been trying to determine for a little while now.