First of all, "organic farming" doesn't preclude you from treating sick animals with antibiotics, if necessary, nor does it prevent you from vaccinating. (Sick animals are required to be held back for a specified period before entering the food chain.) What it does attempt to prevent is animals being fed prophylactic antibiotics, which is a major cause of antibiotic resistant bacterial strains.
Second, organically raised animals are not festering with disease. My wife and I have hundreds of healthy, organically raised animals on our farm. For example, in the last summer we have grown, processed and sold over 500 chickens which we have lost ZERO to illness.
Animals raised in humane, low stress (and the low stress is key) situations GET SICK VERY INFREQUENTLY. It's in situations where they are concentrated in industrial settings (ie. chicken broiler barns or cattle feed lots) that the stress kicks in, suppresses immune system function and you end up with sick animals that get fed antibiotics to cover up the symptoms.
Sorry.
I'm far from an expert but this has been an interest of mine for years -- deeper than just watching Food, Inc.
You're right that livestock in feedlots carry awful diseases. But in proper conditions--you could even say humane conditions--they don't inherently carry any more diseases than you or I.
I mean, what are you arguing for exactly? That we shouldn't use natural sources of NPK? Try your hand at explaining that.
I don't eat crops fertilized with human feces, either.
"That we shouldn't use natural sources of NPK? Try your hand at explaining that."
I don't like famines that kill millions of people.
A couple more:
http://en.wikipedia.org/wiki/List_of_famines
Note how few of these occurred in countries with industrialized agriculture (the exceptions being cause by war devastation or the like).
https://www.google.com/search?q=percentage+of+population+in+...
Numerous sources demonstrating that pre-industrial farming resulted in 90-odd percent of the population being peasants.
That was the norm essentially everywhere on the planet right up until the development of modern, mechanized agriculture.
Click through a few of these and note how many of them are spread by animals in living in a low density, no antibiotics, natural diet environment.
Animals raised without antibiotics and vaccinations carry a horde of diseases.