While I think the OP's reaction was pretty strong they are legitimate complaints about some of the quests feeling unfinished when it comes to animals. Might be a side effect of pet pal requirements leading to these quests not getting the same polish as other side quests.
Though I think something was missed in the discussion in comparison to OS 1 - in my opinion the sanctuary where you find dozens of slaughtered animals who were pretty much defenseless against the immaculates was far worse than anything I've found in OS 2 so far. The problem at that point was there wasn't a good enough motivation for killing them by the immaculates to justify letting it happen, at least to that degree. It's confirmed later on that the Immaculates kill animals for their bloodstones but this should have been established before getting into that sanctuary. Then Icara doesn't mention it at all after that, and you can't tell her about it either.
I think the solution for any writing problems would be to give the player the dialogue choice to show they care for the animals that are suffering and have options available to you that are plausible. That sanctuary situation could have been handled better if, as mentioned, the motivation for killing them was established and Icara shows some reaction to the news, and also able to save that family of wolves or at least a few other animals aside from one boar. For the bear cub in OS 2, just giving the option to respond to the cub's reaction, like trying to convince it to live on its own, or putting out of its misery, as options. Emmie would have been very simple, give the option for them to meet and if Emmie is too far gone and kills Buddy that would feel finished. That cat - yeah, just have the dialogue option to tell it what happened to its owner.
In summary, give as much attention to pet pal related side quests as other side quests do.