I seem to remember not sacrificing a chicken for the blood stone; and not allowing Roy's menagerie being taken for the slaughter. I did allow the chef to catch his errant chicken, and was scolded for it. I also used a blood stone to help the beast of burden thingy that looks a bit like a guar. Other than that, I'm slightly lost, unless you're referring to actually aggressive animals, though for the most part they could be avoided.
I also have no idea what the original poster is complaining about. I seem to remember having the opportunity to save/spare animals more often than not during my adventure.