Many thanks for posting this summary. I should have taken the time to do my research more in depth, but I am not surprised that groups like PETA have co-opted a reasonable point of view and distorted it to fit their narrative (which is usually about narrative over fact). 

I would like flesh out (pun not intended) your point about animals suffering in farming. Agriculture has gone through many revolutions in the past, including products of the industrial revolution, like milking machines and tractors, through to genetic and agronomic breakthroughs like the green revolution. Being privy to a lot of what's going on in the industry right now, I would say we are currently undergoing a welfare and environmental revolution. 

As far as livestock are concerned, we have gained a lot of knowledge about their genetics, biology, nutrition, and health needs in the last 30-40 years. Even the worst farms have arguably more balanced nutrition for their animals than the average North American person's diet. With that being said, we have neglected the behavioural and welfare aspect of raising animals, and that is an exploding area of research, that is also being taught to agriculture and veterinary students alike. As @baerdric correctly pointed out, Templin Grandin is an icon and pioneer in this area, but the ball has kept rolling since then. I personally predict we will see massive changes in the next decade or so in how we house and care for animals.