there's coyotes and you can shoot the fuck out of them 

Cows, and dogs.

There are "Brahmin," which are essentially two-headed cows. In "sneak" mode you can actually activate them to push them over. I'm pretty sure India's Fallout versions actually remove brahmin entirely due to cows being religious over there.
 
There are also geckos and dogs. After you kill them you can collect their meat and hides (not reflected visually in actual gameplay, as in you don't see them skinned or cut up or anything.) 
 
Basically if it walks, you can dismember any of its limbs. (So you can shoot dog/gecko/cow heads off, legs off, etc.) 
 
All the ways to "be cruel" to them straight-up have to do with killing them. There isn't any additional means to be cruel to them, and what you can do to animals in the game is no worse than what you can do to other human beings. So relative to the game they have pretty "equal" treatment.

Looking at this page, I appreciate the fact that Animal Crossing is also listed as a game that features animal cruelty.

What kind of thread is this!?

There's no animal cruelty in video games.  They're not real animals.

" There's no animal cruelty in video games.  They're not real animals. "