I have also noticed there seems to be a fair amount of bad stuff happening to animals in the game. I mean, the first time you get to use pet pal is on the dog on the boat with you and there's nothing you can do for the poor scared dog, and the dialogue actually has an option for killing it.
The black cat and buddy were both refreshing uses of pet pal after the first impression you get with it, and the crab on the beach was also relatively light-hearted. The black cat has a happy ending, but not being able to help Emmie really sucked. Maybe it was meant to suck though, because Emmie is the reason why I show absolutely no quarter to any Magister I meet.
Poor Peeper though. Why did he have to kill all of the other chickens?