I fully appreciate your perspective and I agree that the waters are getting pretty muddy when you start trying to tie an IP address to a person, but the issue here is the issuing of the subpoena and not letting Malibu Media pursue discovery. They must be allowed to protect their rights in civil court, and that means they must be allowed to subpoena third parties for information so they can move from "John Doe" to an actual name and in this case, that takes a subpoena from the court.
While your argument for discovery has some logic to it, it is based on a false assumption of fact : that Malibu Media, once it obtains the name and address of the internet account subscriber, will serve a subpoena on that person in an attempt to find out the name of the person who should be named as a defendant.
Malibu Media's uniform practice, once it gets the name and address, is to immediately amend the complaint to name the subscriber as the infringer/defendant and then serve a summons and amended complaint, not a subpoena, on the subscriber.
This is in every single case .