This article and the DEA doc is confusing. It seems to mainly be saying that having a warrant to intercept cell communications won't get iMessages because it doesn't go through the cell carrier.
It's implied a bit that it is encrypted end-to-end and that Apple can't get the contents... but it doesn't seem to actually say that anywhere. This comment on StackExchange says the encryption is only from sender to Apple and Apple to recipient, so Apple has the plaintext: http://security.stackexchange.com/questions/18908/the-inner-...
Also, wouldn't the same issues have come up with BBM?