The film maker in me would say "And who made that documentary, and what agenda were they pushing?"
Whether or not there's a few bad eggs, looking at the link in the original post, this is to prevent eco-terrorist type groups from infiltrating, disrupting, and attempting to harm damage or destroy otherwise acceptible companies.
It is a growing fad these days.
Heck, somebody somewhere even paid off the writers on the TV show "Bones" to harp on chicken farms so bad I wanted to vomit (not at the content, but at how blatantly PREACHY and obviously misleading and clearly transparent the attempt was -- pathetic, bones writers, pathetic!). There's no doubt some advocacy group sponsored that episode.
It's getting bad. These wannabe-activist folks don't realize that the human being evolved as an omnivore, not as an herbivore. They don't seem to realize that without humankind's need for food there would be no cows in North America at all, for them to fret and fawn over. Without the ability to package and process food (like, say, meat?) society as they enjoy it wouldn't exist. We'd be back to hunting and gathering (gasp! I mean.. just "gathering" -- can't harm animals in nature, now can we?)
I'm not saying I'm for unethical treatment of animals or anything. I'm trying to present the other side of the coin. Do I think it's perfect? No. Do I think it's as portrayed in such villifying documentaries? No.
You can't really judge it without taking into consideration in regards to this history of the trade. You have to look at how we used to do it 100 years ago and follow the progress of the trade as it got better and better, AND the impacts this has had on our entire society. Often times you'll find some inflamatory "thought inspiring" production that only focuses on a narrow slit of the here and now.