I'm reading the Unsettling of America by Wendell Berry right now and one thing he points out is that that by removing the human from the process and focusing only on the inputs and outputs, efficiency and productivity, we get unintended consequences. Such as how a totally sterilized system which removes all trace of all disease would also remove any opportunity to build disease resistance in human beings.

Not to mention the how of it. The traces of antibiotics that disrupt your gut microbiota, the trace levels of pesticide and plastics of the packaging, etc.

When it comes to animals and meat, there's at least another biological system in all its complexity dealing with all of that shit first, and what you get out the other side is more pure food than the alternative, eating the plants directly.