In other words, how much of negative effects of meat from a spiritual level are actually the result of an unnatural/non-sacred way of obtaining it? Is there any suffering occurring if an animal lives its life connected and in a natural environment and then at the end of that life it is consumed vs decomposes via fungus, insects and bacteria?
You are only speaking of one single factor here which is nevertheless an important one. That is the suffering of an animal. Any creature can die a painless death if subjected to certain substances that would kill us without pain. Does that make it right to do so? Humans themselves can live in a “natural environment and then at the end of (their) life be consumed vs (decomposed) via fungus, insects and bacteria?” Following this line of reasoning resorting to cannibalism would also be acceptable.