Actually, there isn't a noticable loss of audio quality when it is recorded over the phone. When Al Gore recorded his lines for Futurama, he did it over the phone, I believe.
We do this at my studio, it's called a "phone patch" and sounds remarkably good considering the source.
They are recorded through that same pro equipment (ProTools HD Accel) we use for studio recordings. With a bit of eq and other adjustments it actually sounds just fine.
For a commentary track I doubt anyone would notice the difference.