I thought there was an option for that before. Maybe in the plugin from Boroda74?
A workaround for this could running MB inside Sandboxie, so you would have only the modified files twice, being the ones shared untouched.
Anyway the really revolutionary good solution for this would be asking to the utorrent developers to treat the audiofiles by the checksum of their audio stream, and not by the checksum of the full file as the song files are only containers.