We figure as long as it can be profited from or paved over, it's justifiable. It's not.
One day mankind will grieve because of the suffering we have caused animals. But by then it will be too late.
That said, I can't even kill spiders. It doesn't make any sense but I've an unavoidable feeling of guilt if I don't release them outside unharmed. Yet I have no problem eating meat. My empathy is irrational.
Empathy is irrational, since it relies on identification with the other being. It's always easier to identify oneself with a living being than to a piece of meat.
On the other hand, it's also very rational; it's a much better strategy than if it was guided by pure knowledge, since it optimizes cooperation: otherwise, you'd either be completely indifferent to someone you can actually help (e.g. injured person near you) or live in mental anguish by the fact that you know that thousands are constantly being killed by wars, curable diseases, etc.
[1] http://en.wikiquote.org/wiki/Joseph_Stalin#Misattributed
Instead of the way you've been thinking about this, suppose instead that empathy is a straightforward consequence of mirror neurons, which essentially try to model the mental state of others based on their behavior. That might be most useful when dealing with the others in the ancestral social group, but it might also be useful to figure out that that bear over there is probably just protecting her cub, while the tiger last week was probably just hungry, for example. Of course, it would have to be possible to override empathy fairly easily, even in the context of one's own social group, but in the absence of any particular reason to do so empathy might in large part guide one's behavior. Stick people in an environment where food comes from the store, nothing wants to kill and eat you and the animals you encounter most are domesticated or mostly acclimated to humans and one can see how empathy might be applied to all kinds of things it wouldn't be under other circumstances.
This is just a half-baked hypothesis by an amateur, but you get the idea. Brains end up just being good enough, not optimal. If anything, it's a wonder that ours aren't even worse than they are at general purpose computation.
Empathy is the antithesis of power. That's why it will always be the exception in humans.
Are you referring to the Halo Effect? (http://lesswrong.com/lw/lj/the_halo_effect/)
Edit: I don't think I meant the Halo Effect - there was another kind of bias I read about on lesswrong.com, but I cannot find it.
Rat 1, Human 0 ?
Because animals are not humans, and trying to raise animals to the level of humans does not do that - rather it lowers humans to the level of animals.
As much as you have compassion for animals don't confuse them with humans.