How about building in any of the areas not in green?
I think the City Hall/ Market/ Van Ness/ Upper Market Castro would have been a great place for the tallest buildings (outside of the green zone of course). It would look great up against Twin Peaks as a backdrop. It also has MUNI and BART access.
SF hasn't had a major quake like in 06 and there was nothing near what the financial district is now. Imagine the 06 quake today, or worse.