disabling streams in quicktime movies with ffmpeg In Quicktime pro you can turn off streams in movies, without deleting the stream. Is it possible to do this with a command line application like ffmpeg?

I have a bunch of video files that were recorded with both the crappy on-camera mic and a separate audio recorder. I've synched the sound and added it to the video, and now each clip has two audio streams. I want to keep the original audio, for reference and archival purposes but disable it. It's obviously done in metadata, but can it be done by ffmpeg?
QTCoffee let's you edit track information in QuickTime files, but it's OS X only and donationware:

$ modmovie -list clip.mov
Track list for clip.mov:
    * Video Track
    * Timecode Track
    * Sound Track
$ modmovie -disable "Sound Track" -save-in-place clip.mov


If you are on OS X, and if you have QuickTime Pro (included in the pro apps), I would rather use that and AppleScript.

For other platforms: libquicktime can also edit track properties through it's API, so you will need to write a command line wrapper first ...