Conspiracy? Nah, cockup.
So, the author of the source article is an idiot. The "separate contacts" thing in iOS is an iOS 6 BETA thing (I can tell by his screenshots); FB is just one more source of contact info, and the iPhone seamlessly combines them where it can, but where there's not a matching email address it cannot, and leaves them separate. Of course you can't delete them, can you imagine what users would say if you could unfriend someone accidentally from your phonebook?!
I wonder if the email addresses thing is similar, too. What if you didn't enter those emails yourself, but they were linked from the person's Facebook account? Once they're made private (as Facebook recently did), they disappear.
Basically, Facebook can't win. They usually get stung for not respecting privacy, but this time we tell them they've made things inconvenient and shouldn't have done it? I loathe FB and suspect their motives as much as the next man, but that source is unfair, uninformed tosh.