the story had Scootaloo as a changeling and she had to choose between her friends or her family
it ends with her last rites after she was mercy killed

Sweet Baby Chrysalis, that doesn't sound like a fun story.

I was pretty sure I knew what story you were thinking of until you mentioned how it ended. Holy crap is that bleak.

(... I just found out the story I was thinking of - Quorum Sensing - has a sequel. I am afraid to read it.)

Wooo boy, I have no idea what story that is and I really hope someone finds it for you so I can avoid it. Although a part of me is curious how choosing between friends and family can lead to some situation so bleak that getting killed is a mercy.

6528874
cause in that story, changelings need their horn to sense and feed on emotions, and Rainbow ended up breaking her horn off
edit: found it https://www.fimfiction.net/story/24217/for-mother

Yikes.