Twilight is a carnivore, obviously!
...Hmm, how does Equestria handle meat eaters, anyway? Outside of the fish Fluttershy killed, I don't think we've seen any others ever eat meat.

Then suddenly you realize...Decade.
http://fc03.deviantart.net/fs70/f/20...75-d68t9vg.png

When did she kill a fish?
As to how they handle it...if you read fanfiction, then you'll get a non-cannon explanation. (The explanation from the fanfic I read, which was about Kaji Tastumi from Persona 4 finding his way into Equestria...explained it when he was eating with the Mane 6 and the Princesses in Canterlot Castle, and he asked "So...where's the meat" and I believe Twilight got upset that he would assume that there would be meat, and Celestia explained to him that preparing meat would make their cooks very uncomfortable, and that they just don't eat meat.)

:lol

I remember reading a fanfic where Luna loves eating Bacon and when one of the mane 6 found out they fainted.

When she fed the weasels/ferrets in Dragonshy.
http://images.wikia.com/mlp/images/7...rets_S1E07.png

O_O

She also leads a doomsday cult and brightly burns bouncing baby bunnies. Killing a herring hardly seems horrific.

Have I mentioned I love that Fandub?

There is no solidified evidence that Fluttershy killed the fish or worms in this episode. We just see her giving something that looks like fish to a family of weasels from a basket. The same applies for the "worms" that she gave to the baby birds.

True.

Except they can't just "Look" like fish. Ferrets aren't omnivores, they're obligate carnivores. She had to feed them real fish.
Feeding them fish that died of an unknown cause would be rather dangerous of Fluttershy to do.