Well, you did not like my idea...
In the end, this is probably a two step process... First would be to get the USB communications functional with CHDK. Second would be to figure out how to (at high speed) replace the microphone digital data stream with that of the the USB data stream.
As far as I know, nobody here (in CHDK land) has figured out the software interface for the USB controller (where the ports are, what they do, interrupts, DMA, Program I/O, etc.)...
If this is something you need--somebody--will have to dive into a camera and code to figure the whole thing out. May even need to sacrifice a camera to scope/probe the USB hardware to understand what is happening and identify the section(s) of camera code that communicate with the USB port.
In of itself--I can imagine getting control of the USB port is the next big break through the CHDK community is waiting for.
And, even once that is done, how to get an external data stream in at high speed (while video is also being processed) and connected to the digital audio stream will be another (probably large) project.
And even if (or when) part 1 is done, part 2 may not even be possible (especially at high quality sound bit rates).
I believe that this all started with a firmware upgrade from Canon for one of their earlier cameras--that was reverse engineered--to figure out the starting point for CHDK.
One of the old timers here may know if that code had debugging labels/symbol tables attached which could make the great USB hunt easier?
-Bill