As in http://www.joelonsoftware.com/items/2009/11/01.html you presumably want to make a web app that people are passionate about.
I would love to use a web app that exposed me to original scores, but noteflight is a unusable wasteland to me. It seems everything is a transcription of Iron Man or the Titanic theme. I don’t care about that crap. If i want to hear a bad midi version of those songs, kill me, I’ve gone retarded.
I acknowledge lots of your users do use the site to post these transcriptions. I’m not saying ban them. Just make a simple checkbox or something that users can indicate if their score is original or note.
Don’t alienate the transcribers, this isn’t an either or decision. Just give me some way to use the site the way I want to. Give us a way to signify that a score is original.
The people who care, who are passionate about original scores, will use this feature.

I don’t think that’s enough because 1) I want people to comment on my scores, but don’t want my scores edited. 2) If it’s attached to a particular spot, and that spot changes, the comment is no longer relevant. Does it then disappear? Who can delete it?
I don’t know how hard it would be to integrate something like http://disqus.com/ with your site but maybe something like that?