I disagree. When the Ethereum protocol changes as a consequence of a weakness in the DAO, they are essentially the same entity. I agree that the point of Ethereum is to be the lowest layer protocol, and thus independent from what runs on top if it (like the DAO), but this clearly isn't the case when the core protocol changes as a result of a bug in an app running on top of it.

So after the U.S. government bailed out banks, did you deduce that "USA" is the same entity as "Bank of America"?