Absolutely, the broad system of conventionally raised livestock and other animals is horrendous for both the animals and the environment. I'm 100% opposed to the current system, and I've already read more links like that than I can count.Here is the evidence from the peer-reviewed literature on raising and using animals for human consumption:
The livestock sector emerges as one of the top two or three most significant contributors to the most serious environmental problems, at every scale from local to global. The findings of this report suggest that it should be a major policy focus when dealing with problems of land degradation, climate change and air pollution, water shortage and water pollution and loss of biodiversity.
Livestock’s contribution to environmental problems is on a massive scale and its potential contribution to their solution is equally large. The impact is so significant that it needs to be addressed with urgency.
ftp://ftp.fao.org/docrep/fao/010/a0701e/a0701e.pdf
Plant-based diets in comparison to diets rich in animal products are more sustainable because they use many fewer natural resources and are less taxing on the environment. Given the global population explosion and increase in wealth, there is an increased demand for foods of animal origin. Environmental data are rapidly accumulating on the unsustainability of current worldwide food consumption practices that are high in meat and dairy products. Natural nonrenewable resources are becoming scarce, and environmental degradation is rapidly increasing. At the current trends of food consumption and environmental changes, food security and food sustainability are on a collision course. Changing course (to avoid the collision) will require extreme downward shifts in meat and dairy consumption by large segments of the world's population.
http://ajcn.nutrition.org/content/100/Supplement_1/476S.long
The consumption of animal-sourced food products by humans is one of the most powerful negative forces affecting the conservation of terrestrial ecosystems and biological diversity. Livestock production is the single largest driver of habitat loss, and both livestock and feedstock production are increasing in developing tropical countries where the majority of biological diversity resides. [. . .] Livestock production is also a leading cause of climate change, soil loss, water and nutrient pollution, and decreases of apex predators and wild herbivores, compounding pressures on ecosystems and biodiversity. It is possible to greatly reduce the impacts of animal product consumption by humans on natural ecosystems and biodiversity while meeting nutritional needs of people, including the projected 2–3 billion people to be added to human population.
http://www.sciencedirect.com/science/article/pii/S0048969715303697
Click the links to conduct further research.
Using feedlot cows as the worst example, they fatten them up quickly towards the end of their lives with corn and other grains rather than letting them eat grass. They have to grow an enormous amount of grain for this and waste tons of water, and those monoculture farms growing all that grain are bad for the soil. The cows get sick eating the grain, can get each other sick by being so close together, so they have to give them preventative antibiotics. The whole feedlot is so aesthetically ugly that they're strongly hesitant to even allow filming in it.
In contrast, grass fed cows, raised on farms in areas of natural grasslands, using modern rotational grazing techniques on farms, are fine for the environment. Permaculture farms often include natural ponds for collecting rainwater. Farmers can actually reverse desertification by using modern rotational grazing techniques, since it can accelerate growth of the grass when performed correctly. They're almost fully self-sustaining, requiring very little external input, which is good for the environment and increases food security due to being so decentralized and locally adopted. Compared to endless fields of grain, dense grasslands hold a lot more water, carbon, and nutrients in the soil.
Chickens, goats, sheep, turkeys, and a variety of other animals can also be used on various types of permacultures, whether they're grasslands, orchards, etc. When the farm is designed to mimic nature, to make use of the natural relationships between plants and animals, the animals are contributors to the system rather than just an environmental cost that comes when animals and plants are farmed separately.
Here's a farmer explaining modern rotational grazing:
Examples of reversed desertification with modern rotational grazing:
What you posted is otherwise fine, but it doesn't actually address my argument. None of that has anything to do with permacultures; it has to do with Big Agra factory farming. Permaculture farmers, including the ones that raise animals, are opposed to factory farming.