How Do I Disable the Webcam on an External Thunderbolt Display
Apple don't provide any way to control camera devices centrally, it is left up the program in use to provide the ability to choose.

Generally, well written programs give you a choice, and poorly written (and, generally, poorly supported) programs don't. (Photobooth, I'm looking at you.)

The only way I know to force a program to not use a camera is a hack that's been around a while and that is to use something like iChat to make the other iSight busy so it's not picked up by any other program.

Another, older, hack is to remove the kexts that support the devices, however, that would stop all the iSights from working, so, in this case, not a good idea.

So, in the end, there's no answer, but I'm sure there's an app that people would pay for in there somewhere.