How does he feel about landline phones? The entire thing is just as closed source as Skype and even more easily monitored. And assuming he is okay with landline, would Stallman call a cellphone? What if it was a free software cellphone?
It wouldn't be hard, and certainly not a capacity strain, to get some old modems and haul encrypted PCM in realtime across them. Or even to roll your own PSK/FSK standard to transport said PCM over. There's no packet format or anything you're necessarily limited to.
As for cell phones themselves, I can certainly see the threat. Even without going into Batman-esque theories of someone putting malicious software on your phone that activates the mic when it's idle, it's well known that the cellular networks make extensive use of GPS capabilities. With access to an operator's network, it would probably be relatively trivial to build a very detailed history of someone's whereabouts.