Apart from inhumane, immoral, unhealthy meat production, subsidized corn being sold at below the price of production and screwing everything up is the root of many of the issues in Food, Inc. GMO soy from Monsanto is the other biggie.
Go to eatwild.com and find a local source of pastured meat, dairy, and eggs. Anything you can't find locally can be found (at a premium of course) at Whole Foods or similar. We have a CSA that we get meat and eggs from, and a nearby farm that we go to for dairy. Another common route you can do is buy a chest freezer if you have the room (ours is in the garage) and buy a half-cow or half-pig from a farmer. They'll give you all the cuts frozen and it'll come out way cheaper. Our quarter-cow last year came out to around $4.50/lb after everything, and that included ground beef, steaks, roasts, all the beef we could want. Far cheaper than $30/lb grass-fed ribeye steaks from Whole Paycheck.
Any animal products we can't get directly from farms (cream, butter, beef gelatin, etc) we'll do our homework and find retail products that are organically/ethically produced. Kerrygold is a great brand of grass-fed butter, and our Costco stocks it for way cheaper than any grocery store near us.
For seafood, exclusively buy wild-caught. Salmon aren't supposed to eat corn either.
The best other way to "vote with your dollars" on the issues raised in Food, Inc. in my mind is to completely avoid corn and soy (and anything containing them, ie most processed foods or cheap sauces/similar). Corn and soy products are also not exactly healthy. If we get corn, it's from a local badass farmer that we know, and when we buy soy sauce we get certified non-GMO. Neither are frequent purchases.
Organic produce (from the grocery store) is really quite low on the list. We'll usually buy organic of the dirty dozen when we can (
http://www.ewg.org/foodnews/), but that's about it. Even the benefits of that can be argued. USDA organic produce still has pesticides, just different ones. If you find a CSA or farmer's market where you can actually talk to the farmer, you can get real organic produce without ANY pesticides or herbicides. That's what we had last year with our veggie CSA (farmer moved at the end of the season) and it was wonderful. We got fresh veggies straight out of the ground with a little dirt still on them. You can also grow your own, even something small like a tomato plant or some herbs. I hope to do more of that once we move next year.
Being healthy and ethical is very Mustachian. The key is to optimize, as always. Buy in bulk when you can, shop sales, make everything you possibly can from scratch, and don't buy junk/"snacks". Don't be someone that grabs anything that has the "organic" label slapped on it, or organic sliced watermelon for $9/lb. That's a great way to get your grocery bill well into four figures. Frugality is only at odds with organic if you let it be.