I could go for Flutter-Bat being a villain of the kind you describe. The comic already established that Flutter has some rather odd ideas of what is fascinating when it comes to her animal friends. And I have always assumed that, as Ponyville's resident animal expert and pet raiser, she has probably had to put down more than one animal to end it's suffering (As I had her say once in something I wrote "Sometimes, helping and animal in their life means helping them to leave it."). It actually could be very interesting.
In other notes
1. Haha Rarity in a Hazmat suit. Guess Equestria has a higher level of tech than we thought, if they need Hazmats. Or is this more leftover tech from the human collapse theory (come to think of it the suit actually has a biohazard symbol on it, so they also have to have out method of warning nomenclature. More proof of a previous human collapse.
2. Pinkie's mane is prehensile? No, I take that back, Earth ponies manes and tails in general are prehensile (Flutterbat was hanging by her tail, not her back hooves)
3. In the flashback to the last apple infestation, there was a pony who seemed to be wearing a hat Identical with AJ's. This seems to bolster my theory, that the reason AJ seems so attached to her hat is that it is a hand me down and a family heirloom (I always said it was her Daddy's hat, but with this flashback maybe her it goes back even further). Actually, since we don't know exactly when the last infestation was, or at what age Granny stopped wearing the poke bonnet, we just may have gotten our first glimpse of one of AJ's parents
"For I have heard the Song of War, and to me, it sounds just like "Please, Mister Custer.""
Cogito Ergot Sum, "I think there is something wrong with this rye bread." (Aplogies to Seafrol.)