To stop FaceTime from encoding video when in a call, make it fullscreen and it will move into its own space. Then switch back to your main desktop space with a four finger swipe to the right (or by simply switching to an app in that space). Although your camera LED stays on, this actually pauses the video, reducing your CPU from 100% to around 20%. You will also find that voice quality improves with less drop-outs and cracks because now your CPU is prioritized on encoding audio.
Update: As mentioned in the comments, it's seems to be sufficient to just have FaceTime in a space and move to a different space, or to minimize the FaceTime window to the Dock.
[kirkmc adds: I don't use FaceTime often, choosing rather to use Messages video chats or Skype, so I can't confirm whether this CPU usage is universal.]

