A lot of people think there is a real difference between killing a bacterium, an insect, or even a fish, and killing a mammal like a cow. Many of the more complex creatures we eat are indeed capable of limited thought and emotion, though they are not self-aware by any test we can devise. (One can make a case for apes, dolphins, elephants, and possibly others; but these aren't generally eaten.) In general, carnivores are "smarter" than herbivores, since it takes more brain to outwit your prey than to simply find and eat a plant. Dogs and cats, for example, are unusually smart, as far as animals go. Most of the things we eat are herbivores--not as smart, not as close to self-awareness.
Having the biggest brains and the most complex thought in the world does carry with it a great deal of responsibility. When my cat brings down a mouse, she doesn't understand that the mouse can feel pain. For that matter, most likely she isn't aware that she herself exists to feel anything; she's just aware of the feelings. (Think "metacognition". Cats can't do that. For them the world is sensation and action, not self.)
On the other hand, when I'm at the lab (summer internship with pharm/tox department at a university) and we've reached the tissue-collection stage of an experiment, when the mice have to be killed, I'm aware that a mouse very much like the one my cat catches can indeed feel pain and fear. We can even measure the animal's stress level. That's why, when we plan the experiments and euthanize the animals, we work to minimize distress of all sorts. If we're going to kill a mouse, we won't do it in a painful way. If a mouse is subjected to surgery, it gets anesthesia and painkillers afterward. The mouse isn't aware that it exists; so it's not aware of death. Death can't cause distress for a mouse. Pain, fear, and other sorts of stress, on the other hand, are very real for the mouse. That's why you work to minimize those things.
You simply can't get a plan past the animal use committee without explaining how you're going to minimize pain and distress; and if you change the plan without approval, the institutional veterinarian will take it very seriously and might even get you fired, if it's bad enough. The housing for the animals has to be humane--about the size of the cage you'd keep a pet mouse in, containing something the mouse can hide in (usually some shredded paper). The conditions have to be humane--no intense heat, freezing cold, deafening noise. In one experiment, we deliberately caused stress for the mice--by cleaning their cages without, as is usual, putting some of the old bedding in with the new (the old bedding is a familiar smell which keeps them calm).
There is a big difference between a self-aware human and a mouse or even a cat. That's why it's OK to euthanize a cat and not OK to euthanize a human. Death for a self-aware species is a totally different thing than it is for a species that isn't self-aware.