I think what is lost in this conversation is that it has turned largely into ethically treating animals and making fun of PETA. Sure, there is a place for the conversation on the ethics of how the animals themselves are treated, but in my mind it's not even close to the more important part of the conversation.
To me this discussion has to begin moreso with the sustainability of it all. Modern mass agriculture has become an energy conversion process. It's all about converting diesel fuel into human calories. Long lasting effects on the environment (and its people) be damned. Yes, meat becomes a hot button because it takes a lot more diesel fuel to grow [factory farmed] cow calories than it does [factory farmed] corn calories. But make no mistake, the way corn/soybeans/wheat are farmed is a massive issue; meat just exacerbates it since such a large percentage of those grains go towards meat production.
The answer for those of us that are willing to be concerned with such things is to avoid factory farmed meat (and grains) as much as possible. Shop as local as possible and as sustainably as possible. I am fortunate enough to still have local butchers and farmers around to purchase from. If I want they're more than willing to allow me to come over and meet the animals that will become my dinner.
Beyond just meat I participate in a CSA for eggs and veggies every year. I get a fresh box of seasonal veggies all summer long. I get dozens of pastured chicken eggs all summer long. In the winter I eat less eggs, and I try to eat as much of my frozen/canned veggies rather than store-bought veggies.
The tradeoff for these practices, as others have mentioned is cost. My chicken costs about $4/lb. Individual pork and beef cuts are much higher priced than the grocery store (although can be quite reasonable if buying whole/half animals). Eggs are about $5/dozen. My veggies cost more. The other tradeoff is seasonality. I don't eat "fresh tomatoes" outside of July/August/September; the rest of the year it's only my canned. I don't eat "sweet corn" unless it's in season, or it's the frozen stuff I purchased locally and sliced off the ear myself.
Obviously, the other big tradeoff is time. It takes a lot more effort to buy local sweetcorn in July, cut it off the cobs, and freeze it, than it does to buy a bag of corn at Wal-Mart. It takes a lot of time to can my own tomatoes. Etc, etc. But by buying locally and processing myself I get much better tasting products, I get healthier products, and it GREATLY reduces the carbon footprint of my family's eating habits.
I understand not everybody can afford to take up the local/sustainable option monetarily, which to me is a societal problem not to be discussed here. I also know it's a lot more work/effort to employ it (and trust me I'm FAR from perfect). But I do think it's worth discussing because the current food system will collapse at some point in the future. Perhaps not in my lifetime or my kid's lifetime, but eventually. The earth cannot sustain the amount of fossil fuels we're currently using, nor the amount of chemicals we're applying to fields in order to feed this level of population so cheaply.
