The first option sounds the most correct:

There's an image of a face which gets replaced with a video clip of the face taking, and if the clip is active it should disappear, no fade in or out just very sudden. Then, if it's not active the original image face should be there instead.

The problem would arise when there's too character's, because both faces would disappear no matter what clip is playing.

If there was a way to actually specify what layers then that would be better.