Um, so let's look back: Germany, 1940s. Where many a German native thought the Jews were actually just being exiled somewhere. And the SS would have gotten away with it too if it weren't for those meddling Allies.
For the story there are a few problems canon wise.
1- Scootaloo was the last survivor
2- Ponies were explained to be the only things that could easily be removed from their Spectra, so plants wouldn't work
3- How did Scootaloo escape when Rainbow Dash already (in your story) stated that no one was going to let her leave (meaning all the armed, not exhausted guards). Also, why didn't they just break Scootaloo's wings in the first place?
4- Rainbow Dash's characterization throughout had presented her as a Psychopath, not a Sadist. Therefore, here idea to suddenly try to torture Scootaloo instead of just kill her seems less prevalent and off character.
5- It doesn't end as well. I know it is happier and whatnot, but 'the police show up an everyone is okay' is a bit less epic than 'the last survivor of a killing spree that caused the gruesome deaths of her last remaining friends; perpetrated by who she once recognized as not just a friend, but a mentor as close as a sister, Scootaloo stares into the face of her executioner (still covered in the blood of the slaughtered children) and coos 'you have beautiful eyes'
Bam! Done! Rounds of applause; cheers abound; roses get thrown on stage. End story. Go get ice cream with the kids.
Jesus still loves your face (and the rest of you), but not every story needs to be happy mic-sunshine. Dichotomies are necessary for the emphasis of both sides. If it wasn't for that nothing would have weight to it. That's why my iPod is stacked with Christian Death Metal and Pinkie Pie Songs, and both Se7en and the Lion King are wonderful movies. Got to have both sides to really experience either.