If you go to the top of the contacts screen, it should say "Contacts: All Contacts". Click it and it should let you choose which contacts to see, like google, facebook, or phone, etc.. But I think you have to do that every time you reopen Contacts.
I didn't like that either. So what I did was instead of signing into Facebook through "My Accounts" I only signed into the "Facebook for Android" app. I can't remember if that linked the pictures of the same friends with my phonebook, but for some reason I had to install "SyncMyPix" to link the pictures. But at least I don't see all my facebook friends in my Contacts. Lol
Try that out and see if it works for you. =)