If I recall correctly, the "Favorites" features were added after the site was up and running,
specifically to address the requests of those who
WANTED alerts when fave authors or stories updated. That is very simply solved by UN-faving everything.
As far as system emails is concerned, though, those are virtually impossible to get out of, unless you wish to relinquish your membership as well. We only send out system emails, however, to alert for the Awards period, or for special, important-to-the-site things, like fundraising. Thus, even without any favorites, you will probably receive a total of 12 to 14 emails from the site annually.
As Mitharus said, however, we have far bigger issues we need to address at the moment than trying to selectively stop system emails.
Again, UN-fave stories and authors, and you will no longer received any alerts regarding fanfiction.
~~Wiccan~~