Could you say more about the difficulties you foresee? I'm guessing that Bloggingheads would have the two separate streams of audio from each microphone, which should make it somewhat easier, but even without that figuring out which speaker is which doesn't seem beyond the realms of what audio processing might be able to do.
I think people just use standard video-editing software to combine the videos and their audio streams before uploading them.
Sweet, there's another Bloggingheads episode with Eliezer.
Bloggingheads: Robert Wright and Eliezer Yudkowsky: Science Saturday: Purposes and Futures