I don't know if there's a way to disable the email invitations. There was at one point in the past, but the idea (from Facebook) is they want you to be able to invite your FB friends to your site OR email users who aren't Facebook users to join your site.. and of course, Facebook will let them know how they should join Facebook too.
We have a task to look into some possible big updates to the Invite module, and if there is an option to disable the emails, we'll include it in a future release.
Good luck!