This is how I went about it... I sync my contacts through GMail and if you uncheck Facebook as a group in your contacts it just leaves my regular numbers with Facebook linked to the numbers I have in my contacts. Best way to go about it IMO.
I dunno. I like Facebook integration. I decided to leave FB contacts on and took about an hours to link FB contacts that didn't auto link. Hopefully iCloud will remember the Links and back them up for future restores and upgrades.