Hi Sean
There's a lot of other info in the article worth reading (criminalization of undercover investigations that help bring issues of unsanitary conditions and animal cruelty to light, and the article highlights mistreatment of animals)- I just posted the headline. Having said that, I agree - the organic industry is far from perfect (especially large scale organics, I much prefer small scale local producers). I'm pretty sure there was an e-coli outbreak due to packaged organic spinach last year. And "organic" apple/pear orchids use antibiotic spray to keep Blight at bay (while I don't like antibiotics sprayed on my foods, if the alternative is blight killing off an orchard in a matter of days, then it seems appropriate and necessary).
And you are right - it does depend on scale. In regard to meat production, overcrowding of animals seems to be the cause for an increased risk of poisoning from e-coli, salmonella, and other dangerous pathogens, which is a problem within the "organic industrial complex" and conventional CAFOs (both are "big ag")
interesting info, highlighting you point. see the article below (from 2010):
When medical researchers at the University of Minnesota took more than 1,000 food samples from multiple retail markets, they found evidence of fecal contamination in 69% of the pork and beef and 92% of the poultry samples. Nine out of ten chicken carcasses in the store may be contaminated with fecal matter. And half of the poultry samples were contaminated with the UTI-causing E. coli bacteria.
KF: Is factory farmed meat more likely to get E. coli out into the market, or is all meat (even free range) carrying that potential?
MG: In chickens, these bacteria cause a disease called colibacillosis, now one of the most significant and widespread infectious diseases in the poultry industry due to the way we now raise these animals. Studies have shown infection risk to be directly linked to overcrowding on factory chicken farms. In caged egg-laying hens, the most significant risk factor for flock infection is hen density per cage. Researchers have calculated that affording just a single quart of additional living space to each hen would be associated with a corresponding 33% drop in the risk of colibacillosis outbreak. This is one of the reasons many efforts to improve the lives of farmed animals is critical not only for animal welfare, but for the health of humans and animals alike.
but the same article goes on:
In terms of other infections like Campylobacter, the most common cause of bacterial food poisoning in the United States, Consumer Reports is publishing an analysis of retail chicken in their January 2010 issue. The majority of store-brought chickens were contaminated with Campylobacter, which can trigger arthritis, heart and blood infections, and a condition called Guillain-Barré syndrome that can leave people permanently disabled and paralyzed. Comparing store brands, 59% of the conventional factory farmed chickens were contaminated, compared to 57% of chickens raised organically. So there might be a marginal difference, but the best strategy may be to avoid meat completely (good reason for this info to be in a go veg thread 
. With the virtual elimination of polio, the most common cause of neuromuscular paralysis in the United States now comes from eating chicken.
the entire industry is a problem:
"There are many industrial practices that contribute to the alarming rates of this disease. Most eggs come from hens confined in battery cages, small barren wire enclosures affording these animals less living space than a single sheet of letter-sized paper for virtually their entire 1-2 year lifespan. Salmonella-contaminated battery cage operations in the United States confine an average of more than 100,000 hens in a single shed. The massive volume of contaminated airborne fecal dust in such a facility rapidly accelerates the spread of infection.
Factory farming practices also led to the spread of Salmonella around the world. Just as the feeding of dead animals to live ones triggered the mad cow crisis, this same practice has also been implicated in the global spread of Salmonella. Once egg production wanes, hens may be ground up and rendered into what is called "spent hen meal," and then fed to other hens. More than half of the feed samples for farmed birds containing slaughterplant waste tested by the FDA were found contaminated with Salmonella. CDC researchers have estimated that more than 1,000,000 cases of Salmonella poisoning in Americans can be directly tied to feed containing animal byproducts."
http://www.huffingto...h_b_415240.html
MRSA has become a serious issue are large scale factory farms, environmentally disastrous manure lagoons.... on and on it goes... the entire ag system needs an overhaul.
That doesn't mean that I don't think organic isn't better, but it's not necessarily more sanitary. 
