It definitely depends on the animal... I don't like when it's non-optional, though. And it's one thing if it's 'kill this not to starve', or 'kill this before it kills you', but something else if it's 'kill five of these guys because some guy said to'... and even with the dangerous animals, I like when you have the option to run.
I feel bad if I accidentally kill a peaceful animal I didn't mean to just because it startled me in an area where I was preparing to face enemies.