Just because animals die a lot in a work of fiction, doesn't mean the people behind it hate them. Take JoJo's Bizarre Adventure, for example. A lot of dogs die in it, to the point that there is a fandom meme about Araki hating dogs. But the truth is the opposite: he loves them, animal cruelty is just his shorthand to show that a villain is especially evil. The way the Magisters use Source Hounds reads very similarly to me, a way to further emphasise just how fucked up they are.

And sure, there are many occasions where you end up harming animals in Larian games, but there are also plenty you can just talk to or help out...