While I love animals, I generally don't mind doing so in games such as Skyrim and Minecraft. Both deal with having to kill animals to survive. You have dragons that attack you if they lay eyes on you, and I'd rather not become flame charred lizard/reptile because I happen to be related to them in a sense. And in Minecraft, you can starve to death if you don't eat. Yes you have grains and such, but meat deals better with your health. Like, it staves off hunger longer than things like bread and baked potatoes. The animals I use as a food source are treated well in minecraft. I have them penned in so the wolves can't get to them easily, and I deal with the wolves that try and attack my critters. Plus I have to tamed wolves that I don't have go into battle because I don't like seeing them get hurt.
In general though, if the critter is an enemy that is trying to kill me or my teammates/pets/critters, I will kill it first/back. If it isn't trying to kill me or any of my teammates/pets/critters, I tend to leave them alone though