I have disabled this option. However, it does have a problem (apart from the fact that I need to use other programs to tag my files); when you synchronise to a device, and it converts audio, it won't tag the new audio files, leaving them untagged for the player!!
I would probably let MJ change tags if I could disable editing tags within the main window (I'd rather ONLY use the little tag window in the bottom left), and if I could change the default tags to my liking. For instance I used to store the release date in the [date] field as YYYY.MM.DD, but MJ did NOT like the dots. I couldn't change that fact, either. I've now switched to YYYY-MM-DD and now MJ displays correctly, but it has ideas on tags that I do not, and I can't change the ones already there.
So those two reasons, at least for now, are why I do not allow MJ to alter tags.