I don't mean to defend them because this move is stupid, but to help you get this back in control: you can go you your about page and set the @facebook email to be hidden. I had done this in the past and they didn't touch it.
No, that's the problem here: I had definitely hidden my @facebook email address (setting it to be visible to only me) when it was first created. After a number of people posted this story, I found that the email address was suddenly the only one showing. That's what is so nefarious about this. I had to go and reselect the options I had already chosen, and the only reason I noticed it was because of the press. Really slimy.
I, as well, have set the @facebook.com address as hidden and set my normal address as visible and public. After the story broke I found my usual address "hidden from timeline" and the @facebook.com address visible.
Does this fix any device synchronization problems, where someone you know had their record of your e-mail address changed to the @facebook one automatically?
It doesn't seem to be clear, as I write this, exactly what is going on there and how much is completely automatic/without consent vs. how much was "expected" behaviour. It's pretty clear that a lot of people aren't happy about it regardless, though. Even if some contact originally got onto your phone via integration with a third party service, that could have been years ago. If you weren't aware that the contact was only remaining there/unmodified because the third party chose to leave it that way, it's understandable that you might be upset if that changed without warning after a long time.