Facebook is months behind anyway so this is somewhat moot. You can easily write a client mail rule to delete these, which will work around both Facebook not updating and no upstream support existing to suppress these emails.

I think expanding the "Email Preferences" panel to include all applications which send mail is probably OK in the long term (we'll have to make some UI changes at some point, but I feel like adding options there creates way less peril than adding general config options, and expanding it into Diffusion is already planned).