Let's stipulate that non-human animals have a "soul," whatever you believe a soul to be.
How to you judge the soul of, say, a raccoon; a creature than has been called the psychopath of the animal world? A raccoon is never happier than when it's slaughtering a nest full of cute, helpless babies. Red-tailed hawks are such a menace to other species that crows make it their business to hound these magnificent raptors incessantly, injuring and killing when possible.
Is there a place for these creatures in your moral paradigm? What solution do you offer for the utterly ubiquitous violence that has been occurring among all these "souls" for hundreds of millions of years?
We manage deer populations, factoring in hunting and other predation, disease, losses to automobiles, etc., and we thus have stable populations of deer. There is no rational reason to indulge some great sadness when a car hits a deer.