Not the fic, but the picture (Which is on the main page) suggests that PINKIE GOT TO LUNA SOMEHOW. (In case if you don't understand; look at the front of her dress)
In case you still don't understand: Luna is the embodiment of the moon, like her older sister Celestia, embodiment of the sun. Pinkie Pie, a mere earth pony, somehow managed to kill and skin the second most powerful being in all of Equestria!
Objection, your honor. It is quite possible unless Pinkie Pie blew up the moon in the process, Luna and Celestia are automatically remade by their respective entity whenever somepony bothers to kill them. Helps explain immortality. When they die, it muddles their memories of the murder afterward, as a side-effect of the knockout cupcakes that others don't live to see. Resulting in Luna waking on the moon, crashing into Canterlot, then forgetting what she was going to scream in Celestia's face.
So Pinkie Pie has a collection of Luna and Celestia bodies in her trophy room, methinks?
This fic came before Discord's appearance... So what happened when he showed up and Rainbow Dash, the Element of Loyalty, was already dead? "Why, Pinkie, you've done a wonderful job!" "Okey-dokey-Discord!"
Pony anatomy (e.g., nopony having thumbs) and The Verse's adherence to it make a lot of the surgery involved somewhat questionable.
How would Pinkie be able to slaughter the unicorns if they could use magic?
Easy, cut the horns off when they were out.
How does one hide horse meat in a cupcake? Furthermore how would any of the herbivorous ponies be able to eat the horse meat cupcakes without becoming violently ill?
Some fans joke that the ponies are made of marshmallows. I don't know where this started, but if they're made of marshmallows then they would be right at home in cupcakes.
Apparently there was one scene where when Rarity seems to almost grab the camera, her hooves look like marshmallows. The idea thus stemmed from that, as far as I know.
This troper has see horses get into dog food and eat it just fine. The key to hiding the meat is "Meat Meal."
Many herbivores, such as zebras, can and do occasionally ingest meat for extra proteins. Hell, there's even a YouTube video featuring a cow eating chickens!
How exactly has Pinkie been accomplishing this act for so long without anyone noticing that at least dozens of ponies have mysteriously vanished under such circumstances? ....Perhaps they believe Krastos The Gluemaker to be the real culprit? A far more pressing issue, however, is this; how have the Cakes not cottoned on to a basement in the store they own and manage daily being used occasionally as a psychopath's murder sanctuary, complete with trophy display? Either the Cakes are away for long periods of time in a predictable fashion, long enough for Pinkie to recover the trophies from wherever she keeps them, set up shop, attract her victim, hack them up (a process which seems to be capable of taking hours), do whatever she needs with the... by-products... and get everything back into its hiding place and cleaned up before the Cakes return? Pinkies preternatural ability to procure and carry things when she needs to aside, lets let Sweetie Belle conclude...
"OH COME ON!"
And all this still doesn't explain where she's getting all those drugs from! Equestria evidently has very poorly guarded hospitals! With a logistics system which apparently centres around "Oh, we seem to be running out of adrenaline, better order some in for tomorrow."