You're right, there seems to be no way to disable the built-in iSight cam on the MacBook/MacBook Pro - BIG mistake on Apple's part! Here's a link to a discussion about this from the Apple forum:
This quote, from the page linked above, MIGHT be helpful to you:
My Logictech 9000 doesn't show up in the Flash video source dropdown for me either. Selecting USB camera just selects the iSight.
However, I did find a workaround: it seems to choose the first available usb webcam, which is typically the built-in iSight. If you have a mac mini with no built-in iSight, it uses the external camera by default. For my MacBook, I found the trick was to make the iSight busy by opening Photo Booth first, then opening the flash chat page. That causes the flash player to find and use the external USB webcam.
Note: your webcam probably has to support the new standard USB Video plug-and-play protocol for this to work, and perhaps only on Leopard.
Of course, have fun trying to explain this to other users of your program... but maybe there is somehow a way that you could code for this, by adding some script that runs the iSight just for the sake of distracting it, before the script runs that is supposed to detect and launch a USB cam as part of your program. Good luck!