This bothers me - not that a Malthusian backlash through pathogen mutation in an overcrowded world is in any way an improbable scenario - because there seems to be an assumption beneath it (though you may not have meant this) that industrial agriculture is rendered inevitable by population increase (see the agro-industry "We feed the world" propaganda to that effect).

Factory farming is not a necessity in view of high population, it's just a money-making operation. The world can feed a higher population than now without it (though we in the developed nations would need to consume less meat, just as we need to consume less energy).