Jon, I don't follow the logic of what you're saying. The panelists didn't consent to having the back-channel comments projected behind them, as far as I know. I didn't consent to it, as a member of the audience. The interruptions were systematic and imposed from above, by the conference organizers.
Bleacher comments should stay in the bleachers while the game is going on. (Note that Miss Manners did not object to chatter which does not interfere with the capacity of the audience to listen to the speakers.) Sure, a spontaneous interruption can enliven the show, and sometimes merits developing into a ritual of audience participation --the equivalent of throwing a home run ball hit by the visiting team back onto the field. But the PDF forum approach was an experiment that didn't work. A lot of what we saw on the screen did not fall into the category of constructive feedback. It needed to be edited, and structured (perhaps along the lines of what you suggest in your proposal), and projected at an appropriate time in the program, not while the speakers had the floor.

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On IRC comments
"Miss Manners's instant feedback is that this particular forum must have done a remarkably bad job of choosing its panelists."
I'm not sure about the PDF forum, but that's often true about a lot of poli/tech forums. But I'll disagree with Miss Manners on some key points here: when you interrupt by voice, you interrupt everybody without their consent. On IRC, people are choosing to participate in a back-channel. It's like choosing to sit in the bleachers.
Certainly, if we want to make a back channel constructive, there have been plenty of suggestions for that. Here's a proposal I offered last year regarding back channel conferencing for promoting good guestions.
If there's a point to rudeness in the online world, it's to hasten feedback-- as instant feedback is now possible. But everybody's used to different paces of feedback.
If you can forward this all to your friend Judith Martin, I'd appreciate it.