Couldn't the server change keys after every message? The delay would be fairly small. Hold the original, change key, retransmit, change key back? Guess that is easily enough mitigated if the client won't allow switching back to the same key.
I guess the point here is: Can there be a backdoor in whatsapp? Of course!
Is there a backdoor on Whatsapp as described on the guardian article? No.
Can the UX be improved to alert the smaller percentage of users that rely heavily on the encryption features when their communication is not being actively protected without disturbing the UX of the rest of the users? Probably yes,
Hell yes! Imagine jusr changing background color and the banner "somebody spies on you." Now it's something like some checkmark somewhere looks a bit different or whatever.. I'm still not sure what when...