Please just stop it with the FUD. If you knew what you were talking about in this situation it wouldn't be bad, but you don't. The current SF store is in a kind of dicey area off Market Street, that isn't convenient to the main high-end shopping district known as Union Street, nor the other really trendy area in town, on the Embarcadero around the Ferry Building. This will close that old store, and replace it with a new, nicer, bigger store in a more desirable location just a few blocks away.
I wouldn't be surprised to see another store being opened later, either in the Embarcadero Center, or near the Ferry Building. But this is not a bad thing for Apple. It's a good strategic move that shows forward thinking.