if a pen register order is made on a provider, and the provider's systems do not readily facilitate full monitoring of pen register information and delivery to the Government in realtime, the Government can compel production of cryptographic keys via a warrant to support a government-provided pen trap device.
as far as I can see, there is literally no way of getting around this issue except by onion routing.
This is sure to drive even more users to TOR, not sure if that's a good thing or a bad thing in the long run.