Indeed, the ##*# directories are MTP crap; by connecting your device (via OF) in MTP mode you can delete them; then shut down while still physically connected but do use the "safely remove" function by holding down the Power button for ~10s. As long as you only ever shut down the OF like this--while connected over USB, by holding down Power to force a shutdown--the default directories will not be rewritten (the same goes for the MSC default directories if you want to delete those too).
Note: Ugly workaround alert.