I love the level of paranoia. The transparent message of these documents is that its possible for The Enemy to exploit everything on your system. "Disable your laptop camera. Disable your computer's audio input."
For the NSA and other top secret uses this makes good sense.
Why not indeed: after hearing that the FBI could remotely activate microphones on mobile phones when no call was even active, of the story of that school that used webcams in Macs to spy on students at home with a special system that disabled the activity light, and knowing the ability for malware to do any of that: Why do I have this camera facing me all day, when I use it three hours a week?
I see, I could be wrong about the particulars of that case. I could see how someone might not notice or be concerned about the light flashing every now and then, too.
If the school wanted to disable it though, it wouldn't be impossible for them since they had access to the hardware. A thin dot of black paint might do the trick, especially if they peeled back the glass a bit, which is a pain, but quite do-able. Certainly something people in the NSA would be wary of... it's a shame that high school students should have to worry about that, too.
If people want something that won't discolor the plastic or leave residue, use the sticky portion of a yellow sticky note to cover the camera. I've been using the same piece of little sticky for 2 years or so.
On Macs it has the added bonus of still letting you see when the camera light comes on.
DoD had a removable device scare a while back (someone intruduced a windows virus into an internal network via one), and for a while there they were going around and filling external USB ports with epoxy. Eventually they "relaxed" their position on that.
They also have a very useful guide focused on network infrastructure hardening. It's intended for Cisco IOS switches, but many of the principles can be adopted to other platforms:
http://www.nsa.gov/ia/guidance/security_configuration_guides...