She killed Sparky.
Given that Agatha showed up with a doghouse without ever having been told there was a dog, it is quite possible that the dog was a magical construct she created for the boys, not an actual dog.
As an example of how this could all work - imagine the entire Hex may be intended as a bit of a cage or terrarium for Wanda, possibly to allow her to work through her grief in a relatively safe space, so that she's not a danger to the rest of humanity. The harms necessary to allow this to happen inside the Hex may be considered better than having her rampage with her powers.
Or, you know, Agnes or others are taking advantage of her to bring a couple of shards of a supernatural entity (Chthon, or Mephisto) into the world. That's always a possibility. It'd be a bit of a turn from comics Agatha, but, c'est la vie.