You seem to be an experienced Mac user who has already considered several good ideas.
If arthur's suggestions or the ideas from http://discussions.apple.com/thread/4709690 don't help you find a satisfactory solution, here are a few other thoughts you can consider depending on how badly you want to eliminate the flashing:
(Apple has changed the built-in camera's name on newer Macs from "iSight" to "FaceTime" and then to "FaceTime HD." Regardless of the name of your Mac's built-in camera, the same info and troubleshooting applies.)
(1) Try to figure out what happened "recently" immediately before your symptom started. Also time it precisely for a few hours to see if the flash occurs at exact, (or nearly so,) regular intervals.
If it is regular, it may be a Skype or other third-party software issue. My Macs never exhibit the problem you describe, but I don't use Skype for Mac. Next time the indicator lights, notice whether you were using any third-party apps while, or immediately before, the flashing. Any bug will be repeatable rather than random.
If it is random, and if you have no other problems with your Mac, the problem may be hardware related. If you are certain you have no camera enabled app running when the flashing occurs, merely restarting your Mac may stop the flashing until next time you use Skype or another camera app. If not, you will likely need professional Mac service.
(2) Hacking of webcam control should not be a concern for Mac OS X users.
If you are using Windows®, you are wise to be cautious and take every possible precaution against Windows®'s security weaknesses, whether running on a PC or on a Mac (and whether via OS X Boot Camp or one of the PC emulators that runs inside OS X.)
For OS X Macs, the only way I know to make the webcam controllable by someone else is for you (or someone else who had access access to your Mac) to modify or somehow damage your Mac or its software. Unless an "administrator" of your particular Mac has installed, activated, and authorized Apple Remote Desktop or some other software for remotely operating your Mac, it is highly unlikely that anyone can be using your cam without your explicit permission and action.
However, if you are convinced that your Mac has unwanted software that you cannot identify, securely erase your entire startup disk. Then reinstall a fresh copy (not from your backups) of OS X and all necessary apps and updates. Finally, copy your important user data files to the fresh system from your backup to your fresh system.
(3) If you've not already done so, you should Safe Boot your Mac. Safe Boot forces an automated OS X disk check and repair routine. If your disk needs significant work, Safe Boot may take several minutes to finish. Do NOT try to use your Mac while in Safe Mode. When your desktop appears in Safe Mode, immediately restart your Mac normally and see if the trouble persists.
(4) You are wise to be concerned about the effects of any camera disabler. While any such disabler will probably not disable your keyboard and trackpad, while in effect, it would almost certainly disable ALL (including any connected external) USB camera functions.
Message was edited by: EZ Jim
Mac OSX 10.8.2