The problem is that if you instantiate a prefab right after the Instantiate() call Awake is called before you can do anything else. It's almost like the constructor. If that's not a big problem you can instantiate your prefab anddeactivate or remove the components you don't need / want like mentioned above. There's a nice way to remove or deactivate only the scripts of an GameObject:

MonoBehaviour[] Scripts = GetComponentsInChildren<MonoBehaviour>();
foreach (MonoBehaviour MB in Scripts)
{
    [...]

}

If the Awake would get you in trouble my approach would be to write an editor script that creates those preview-prefabs in the editor. Editorscripts are so powerful, half of my life is running in the Unityeditor. It's almost like you are in "The Matrix" :D

Use SetActiveRecursively(false) on the instantiated game object so it won't do any script processing.

What if instead of doing this at runtime you make an in-editor tool that preprocesses all of your prefabs and creates _empty versions? You could even write it in such a way that it maintains sync between the main and _empty prefabs. Probably. :)

As a supplament to Ashkan's answer.

If you want to make sure things are unchanged after you have done your stuff and you don't want to have to manually clean everything up, you can use RAII (Resource Acquisition Is Initialization) design pattern:

http://stackoverflow.com/questions/1757089/is-raii-safe-to-use-in-c-and-other-garbage-collecting-languages

The answer near the bottom by '280Z28' shows an example of how to do RAII in C#. It is a good way to change the state of the program/object temporarily. It also helps keep all the state modification code together making it more maintainable.

Can you make a new prefab which is a "base prefab" that is the empty copy, and have that prefab included in the more complex one? Then changes to the base would still propagate to the scripted one, but you have more options about which one to instantiate. (Unless I'm remembering wrong, and you can't composite prefabs).