Apps like Snapchat, deleting the message as soon as it's viewed, wouldn't work when you want to apply a ton of context in the conversation. Too often I'm having a "conversation" on Snapchat but it's more like small snippets of text and a lot of me questioning what the other person said a few hours ago.
From the article, that's the part where Apple could MITM the communication, because public keys retrieved from Apple would be automatically trusted. They can just silently inject an extra public key for which they have the private key. That said, it seems like the protocol at least has forward secrecy, meaning that if they didn't inject a bad key when the message was sent, there's not much they can do later to decrypt the message (unless they have a backdoor that allows them to force your phone to send them its private key)
(And yeah I know iMessage isn't open source and so this is difficult to verify, but "Talk" isn't open either. Apple published a big PDF about how they do encryption - if this were proved to be false it would destroy all trust in Apple forever, so I believe what they say.)
Big PDF: http://images.apple.com/ipad/business/docs/iOS_Security_Feb1... (See page 20)
tl;dr: "Apple does not log messages or attachments, and their contents are protected by end-to-end encryption so no one but the sender and receiver can access them. Apple cannot decrypt the data."