Sounds like a lot of work. But if you rip the video to an elementary stream, you'll have a PCM (wave) file that you can do most anything with, then re-author using the new stream. Keep in mind that it'll be very easy to mess up the audio synch by doing this type thing.
Something like Ulead VideoStudio will allow you to over-lay a second audio track and suppress the main audio just in that portion of the timeline that you want. This will involve re-encoding the video, and some loss of video quality is possible.
Personally, I think I'd just try to deal with it as it is. It's not quite the end of the world.