You're falling for propaganda on your heart string.
Don't want to eat chicken? Then don't eat chicken.
Anybody that cites that food,inc shit should be immediately dismissed as a dumbass that has zero clue to cooking or taking care of yourself. Now go be scared of your food and buy organic because it's so much better for you!
Propaganda? Excuse me, but I had a bunch of family living in Arkansas right now with Tyson chicken farms. Now, they own their land and their chicken houses, but for the most part, everything to do with the chickens is by Tyson. And much of what is said in Food inc is true to some extent on many farms, and fully true on others. In Arkansas at least, my mom's family makes plenty of money not just through the chickens, but from the logging they "loan" acreage out for as well. I have been there, waded through chicken shit, and done things people on these boards can only see about in a movie.
Now take my uncles chicken farm. He owns the chicken barn, but Tyson owns the equipment. They own the chickens as well. Basically chicks are dropped off at one of his barns, and 8 weeks later they are picked up to send off for processing. He gets paid by the poundage of the weight of the chickens. From that pay, he has to buy their supplied feed, and is not allowed to use any other feed. Remember the chickens are not owned by him. He's basically being paid to watch over the chickens. As a chicken custodian, er chicken farmer, it's his job to maintain the equipment, and raise the chickens.
Now the automated equipment does feed, water, and somewhat clean out all the massive amount of chicken shit that is generated. It doesn't get all the crap though. He still has to go through every so often and get is really clean. The chicken poop is then used to sell for fertilizer so he can make some more money. This is where the propaganda comes in. It's up to the farmers to clean out the poop missed by the equipment, and dead chickens that happen. Many of them are lazy asses though and don't bother. So yes, on many farms the chickens get very, very, very nasty wallowing around in their own shit for much of their 8 week life span. And yes, the feed for the chickens contain tons of crap in it to make them grow faster as well. Which is why there are dead chickens my uncle has to clean out on occasion. Since the chickens are genetically engineered to be bigger and have bigger chest, those chests are literally too massive for most of these chickens. They either die because their own body weight keeps them from getting off the floor and out of some poop so they suffocate to death, or their hearts go into cardiac arrest from growing to fast.
In regards to food inc when it comes to the raising of the animals, it is fairly spot on when taken in certain contexts. Which is that of the lazy farmers, and there are more of those it seems than not. As for the processing plants, well I don't have first hand accounts to go with on that.