disabling streams in quicktime movies with 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 ...