An unnatural way to do good to other nature components?

I just had this random thought that being an vegetarian is against the natural design in some way... Some vital amino acids are almost only accessible to us by meat or diaries before supplements were available. Native Americans once had a diet relied completely on maize and their life span suffered from that. That was vegetarian in practice but they were forced to be.

I looked up the history of vegetarianism. Vegetarianism was initially almost always religion or philosophy related. It did not only serve as an attitude but a discipline among a specific community.  Since about late eighteenth century vegetarian population started to grow and became more common without institutional restriction. I see this of as a mark of the civilization of human society because we are only to think about being nice to other beings when survival is not the main concern. I want to say that it seems to me that we have evolved to be able to even think about being a vegetarian. If we are able to choose a diet regardless of our natural biological premise, it indicates a privilege. So even though we are using a non-violence policy to other animals, what exactly is the philosophy behind - Mercy? Love? A repulse to eat the juicy flesh? I know that a lot of times different philosophies yeild the same outcome, but I wanted to bring up this to discussion...