Honestly I think the whole "exploiting innocent creatures" thing is overexxagerated for the fun of it. Yes you can throw them around, yes you can butcher them and leave them to starve, but you don't have to. At it's core the only "necessary" mechanic is having the pals do work for you, which is never implied to be bad. A collectible log even explains that they seem to want to help people and do it on their own without being forced.

Personally I don't mistreat mine as I also prefer the wholesome adventure vibe, when they get angry or depressed I take care of them and pet them, etc. And it's not like mistreating them is an actual mechanic, there's no "slap" or "punish" button, it's just you not engaging with the mechanics to treat them well, if that makes sense.

It does feel slightly jarring to headshot a fluffy sheep with a musket, but is it really worse than having a lvl. 100 Charizard use Flamethrower on a lvl. 2 Caterpie, just because the violence is explicit instead of implied? Feels kind of hypocritical to me.