Um. That would be exactly the point of doing it, in this case. The camera indicator (and the microphone indicator that every laptop should but currently does not have) should be completely inflexible.
What "flexibility" is added by having an indicator that only sort-of indicates, anyway?
As a compromise, the indicator could be wired-OR: software can turn on the indicator if it wants to, and it gets turned on if the camera is on, but software cannot turn it OFF if the camera is on.
Seems like, at worst, any sort of manufacturing inflexibility is solved the same way they usually deal with this stuff: A ribbon cable. Then you just have to worry about the physical security of the machine which is its own independent issue regardless.
Personally, I assumed they did it this way since it seems obvious (that's what I do in my own electronics projects) and much simpler than using a microcontroller to do it. I forwarded this idea to concerned friends. Looks like I'm eating my own words.