If you read the article, you'll note that the author was successful with an attack that demonstrates that Apple can access the plain text of at least recently-delivered messages (and possibly all of the backed up messages).
Apple did a great thing by making iMessage secure by default. They should do a similarly great thing by making iCloud backups secure or by making it very obvious to the user that they are not secure (and what that means for your other "secure" data).
This seems likely given they offer to store your key for FileVault[1] under some secret answers. I think this delivers the same level of "secure" in the sense that, provided they don't store the passwords you submit (possible law enforcement request), then they shouldn't be able to decrypt your iCloud backups either.
Apple can still get at them because they can reset your password on you. Certain files in the backup will not be accessible to them if they were encrypted with a key that wraps the Device UID. iMessages don't seem to be one of these files, but Mail backups are clearly inaccessible.
i think the most important takeaway here is that the reactionary press release "Apple’s Commitment to Customer Privacy" was very carefully worded to give the customer a sense of security. it's definitely not telling the full story, but it serves its purpose of reassuring a concerned user base.
A co-worker and I send encrypted e-mails back and forth occasionally. If he decrypts my attachments and saves them to his hard drive to work with, that doesn't mean that e-mailing them in an encrypted form was worthless.