Is it possible to remove or delete the "Music" folder?
Do you have any indication that the OS will mind if you just rm -rf Music?

As far as I know, iTunes is the only app that uses that directory (at least on my machine, there seems to be nothing else in it).

So if you don't ever launch iTunes again, that directory should never reappear. If you want to guard against accidentally opening iTunes, you can move its library to a different location before removing the directory.