I set all my music files to "Read-Only" because I don't use MusicBee as a tagger - only a music manager. Because of this, MusicBee will only save ratings to the MB db - this I know. I don't know if it already does that by default or not. If not, I agree an option to select would be nice.
If you are worried about MB messing with your tags, just set your files to "Read-Only".