This does not require any sort of universal truth. If we can justify doing something to one species, then how can we evaluate another species to be "evil" for doing the same action as us on us?
Since there is no Universal Truth, then all of the ethical rules that we live by were made up by humans. Many of our specific ethical rules are deeply influenced by our evolutionary history. Again, since we evolved from primates, it is not surprising that our behavior is similar to social behavior in other primates. If we had evolved from a colonial insect, our ethics would probably be quite different.
As a human being, I observe the Universe from a human perspective. I see it through human eyes (which greatly affects how I perceive it). I have the five human senses-- there are things in the universe I can sense, and there is plenty I can't sense. I understand it with a human brain which is wired a specific way to react to the universe.
Even the idea of "pain" is a human experience that might not apply to an alien species. It is not difficult to imagine an alien that either interprets the electrical signals in our nervous system that we call "pain" differently-- it could have a different meaning (i.e. not cause suffering). Then again it is possible that the alien species might not even have the complex nervous system structures that would make them have pain.
The point being is that I am a human being (more specifically a 21st century American human being) which gives me a very unique and specific set of ethical rules that I use to make judgments. These rules are all I have-- but it would be foolishness for me to believe that an alien race with a completely different evolutionary and social history, would have anything resembling the same ethical rules.
I believe that human life is sacred. Yes, this means that to me, human life is uniquely sacred. Human life is more important and special then any other life in the Universe. I have no reason to believe this-- in fact, the word "sacred" isn't defined meaning that this is a subjective belief that can neither be proven nor disproved. I understand this, but so what... this doesn't impact the fact that this deeply impacts the ethical choices I make.
Based on this, I have no problem with saying that killing cows to produce hamburger that I can eat is ethical. Further, I have no problem saying that killing humans for any reason other then the most extraordinary is unethical. We have strange rules about "special" animals-- dolphins, horses for example-- but I don't think that anyone would choose a dolphin's life over a human being's.
. When the Aliens come to harvest our bodies for food and science, I will be completely comfortable saying that they are evil-- based on my firm belief that human life is uniquely sacred.