Hey Eric,
These guys are correct in that Skype, Linphone, FaceTime, Google+ and many other conference or chat programs / apps will turn on your built-in iSight or FaceTime camera if it is available.
You may want to read https://discussions.apple.com/thread/5248432
Just keep in mind if you disable it with permissions, simply running the disk-utility "Repair disk permissions" will make the camera work again.
If you are able to use the terminal program with root privilege enter the following lines using Mac OSX 10.6
chmod 000 /System/Library/PrivateFrameworks/CoreMediaIOServices.framework/Versions/A/Reso urces/VDC.plugin/Contents/MacOS/VDC
chmod 000 /System/Library/PrivateFrameworks/CoreMediaIOServicesPrivate.framework/Versions /A/Resources/VDC.plugin/Contents/MacOS/VDC
chmod 000 /System/Library/QuickTime/QuickTimeUSBVDCDigitizer.component/Contents/MacOS/Qui ckTimeUSBVDCDigitizer
Or these if at 10.8
chmod 000 /System/Library/Frameworks/CoreMediaIO.framework/Versions/A/Resources/VDC.plugi n/Contents/MacOS/VDC
chmod 000 /System/Library/QuickTime/QuickTimeUSBVDCDigitizer.component/Contents/MacOS/Qui ckTimeUSBVDCDigitizer
chmod 000 /System/Library/PrivateFrameworks/CoreMediaIOServices.framework/Versions/A/Reso urces/VDC.plugin/Contents/MacOS/VDC
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To make it work again you can change the 000 to 755 and run the commands or simply run the Disk permissions repair.