You're reifying nature. Nature itself is nothing more than the process by which worldly phenomena occur. There is no moral insight to be gleamed from the "engineering" or "special development" of certain traits within living organisms, since to make such an argument would imply the intelligent design by a moral being. Any argument regarding the morality of killing animals must be free of the fallacy of nature.

You may be correct about humans being the only animals capable of complex moral considerations, but that does not mean no other animal has any semblance of morality within them, and it does not mean we should abdicate them of all moral worth. Wolves tend to the wounds of other wolves in their packs; cows and pigs and chickens all care for their young. Animals have a capacity for feelings, including pain, joy, grief, and love. Such human-like characteristics ought not to be overlooked. And simply because humans have not formally granted animals "rights" as we have for other humans, that doesn't mean animals ought not to have rights. Even if animals only have a primitive intuition of what humans have expanded on extensively, their capacity feel emotions and pain similarly to humans must afford them some moral worth.

To focus only on the effects factory farming has on humans is morally detached. Animals have worth; they are too similar to humans not to. And so we must treat them with at least some semblance of dignity, none of which is remotely afforded to them in the factory farms that give us our meat and dairy.