Now, I think this issue is best split into two parts: treating animals and killing them. The first part is much more clear-cut: many farm animals are treated cruelly (mostly in the dairy and poultry industries), and this should change.
The issue of killing animals is complicated. About a year and a half ago, the magazine I used to work for sent me and a photographer on a hunting safari in South Africa. I went there half expecting to write about the cruelty of man and the beauty of nature; I expected to write about the evils of hunting. Only problem is -- the trip changed my mind. So much so that my vegan editor decided not to run the story (I would share it, only it's in Hebrew and my English isn't good enough for me to translate it all).
1. Pain and suffering
Oh, the hunters (most of them, really) were just as cruel as I had expected. But nature was far crueler. The simple truth is this: no animal dies a dignified death in the company of family and friends. The lucky ones get a bullet or fall prey to leopards. The less fortunate are eaten by hyenas who eat the poor animal, starting at the stomach, while it's still alive. The rest die slowly of starvation, lying exhausted while vultures pick out their eyes and jackals eat their legs.
2. Death and destruction
The main issue, as I see it, is this: every creature, large or small, every organism, living on this planet kills others. From bacteria and plankton to blue whales: their mere existence means death to others. It was once believed that nature is harmonious, that all animals and plants live with one another, each having its place in the ecosystem. But this is false. It was found that if you visit, say, a forest, and take inventory of its flora and fauna, then come back 70 years later, the picture will be completely different. As a general rule, species don't live with other species in harmony. They compete, and some come out victorious. Then you have people. Like all other species, we, too, cannot avoid killing other species. What, you want to eat legumes instead of meat? Well, antelopes cannot live in a field. They can, however, live among free-range cattle. And those antelopes, buffalos and leopards that would die because you want to grow a wheat field will die a far more horrible death than cattle in the abbatoir. You say we turn a blind eye to the pleas of the cows? What about that of the antelopes? When agriculture was invented and people started planting fields to sustain a huge human population, many animals were condemned to death -- and those weren't farm animals.
It's just that we feel disgusted when we see the blood. Western civilization has slowly tried to distance death and gore from our lives. But it's absolutely impossible to avoid it. We can only push it further away from us.
3. Meat
The question of eating meat, while a moral one, is different from that of slavery because of the role meat has played in our own evolution. There is no doubt that meat has played a crucial role (though there is duscussion about the magnitude of its importance). Only meat was nutritionally dense enough to support a very energetically wasteful brain, and said brain evolved (in part if not mostly) for the purpose of hunting animals. It is little wonder that all primitive art depicted hunting. The first stories were about hunting, animals, and the gods, demons and monsters our forefathers encountered while hunting those animals. They were told around the fire where the meat was cooked. Also, there are several cultures that are entirely meat-eaters (the Inuit) and don't consume vegetables at all. To the best of my knowledge there have never been vegetartian societies. Now, this does not mean that the question of the morality of meat-eating should not be asked, only that it touches our very core.
Lastly, I just want to go back for minute to the issue of animal treatment. There is little doubt that chickens in industrial poultry farms are treated badly. They suffer. But growing free-range chickens and cows is so much more expensive (I think). This would mean that only the rich could afford "ethical" meat. Industrial farming allows even the poor to have it. This, however, does not mean that we shouldn't do our best to improve animals' living conditions in areas of the world that can afford it.