This is the reason why my SO is a vegetarian; he doesn't want to contribute to factory farming and does not want to contribute to the environmental effects of meat farming in general. I don't disagree with his stance; rather, I think it's a good thing to be aware of when choosing food. Thus, I typically buy outside of the factory farming food chain.
However, it's easier for me to do so--I have the income now to be able to do it, and I have access to locally grown meat, eggs, and milk (in addition to the usual suspects of fruit and veg). The economics of our current food system often limit people's choices, and many people aren't willing to spend the extra dough to get locally grown meat, milk, and eggs. Factory-farmed meat is preposterously cheap by comparison.
To me, this is an interesting issue that ties right into the idea of "where does your food come from." There is no doubt in my mind that the environmental impact of such factory farming would be limited if more people bought outside of the factory farming food chain, by frequenting farmers markets, greenmarkets, and food co-ops. Not only is your dollar more likely to go to local businesses, but it goes to support a more environmentally-friendly industry, while you still get to eat your meat. Yum, meat.
There is actually a budding movement amongst former vegetarians to support animal and environmentally friendly meat farming. These former vegetarians, like myself, think that economically supporting these kind of farming movements is more important than just giving up meat altogether. The fact is, humans love meat. Meat tastes good. I'm not going to stop eating it, and neither are a lot of people, but we can choose a more positive alternative than taking part in factory farming.
The other upside is you're less likely to be affected by E.coli recalls.