For lack of a better term, would be awesome to toggle a boolean that shows an un-editable version of the hierarchy all the way back to the scene view. With each higher level becoming more transparent, much like onion skinning in many animation tools. Of course when editing the prefab outside of the scene, the scene wouldn't appear. Sometimes placing objects requires seeing other items, making sure everything lines up correctly.
See the entry in the FAQ called "Can we get the ability to be able to use Prefab Mode but edit the Prefab Asset in context of the current scene instead of in isolation?" Apart from the idea of increasing layers of transparency, it seems to be roughly the same concept as what you describe.