Why do you get evil points on the Karma Meter for feeding an imp through a rock crusher? Imps are freaking devils. In Forgotten Realms cosmology, they're literally Made of Evil! How can it be evil to kill one?
Under a certain interpretation of the alignment system, intent and actions matter. Imps are evil creatures, but they're still sentient and capable of experiencing pain, and getting one killed in such a cruel way could still be considered an evil act. It's the same thought process that tends to describe your average Inquisitor type as lawful evil rather than lawful good.
This also explains why you get points towards Good for assassinating the matron mother of House Maeviir in HotU: her daughter thinks she would pull a Face-Heel Turn if the Valsharess attacks, and since you're helping the Seer stop her plans, you've helped the rebels out that much more.