I personally think tying of the soul to intelligence seems a weird distinction. Does that mean that if person goes into a vegetative state, they have lost their soul? Do animals that are less intelligent have a less likelihood of a soul? If you can breed animals without mental faculties are they soul-less? Does the fact that we can't understand if plants are intelligent meant they lack souls? These seem like petty distinctions.
To me there is a notion that life has some intrinsic value to it. In parallel there is a notion that to exist as life, humans have to rely on destroying life. To me these are equally important, recognizing that life has worth but also to exist you must end life. I find this paradoxical duality to be beautiful.
Now from a practical point of view there are social rules for how you end life. So some cultures thought it was ok to eat all forms of life as long as that life wasn't part of your tribe (societies with cannibalism), other societies thought it was ok to eat all forms of life except for your pets (most Americans), some exclude animals based on religious beliefs (pork in Islam and judaism, meat and beef in Hinduism), and some think it is ok to eat all forms of life that are non-animals (vegetarians).
I think its hard for any of these groups to claim moral superiority. The truth is in order to exist we need to destroy life, but at the same time, most can see that life is precious.