Two stories in terms of height, or in terms of levels? Because Runaway Railway at WDW is also at least 2 stories tall in terms of height, if for no other reason than the Great Movie Ride needed the height for its showscenes and Railway uses that. But outside of any catwalks in the ceiling there's only one level to the building.
I'd imagine the use of vertical space will carry over to Disneyland, so I wouldn't suspect offices to be built on top of the ride, unless it were 2 levels but 3 stories. Building offices next door in the same structure seems very possible, though, since the building is almost twice as long as it needs for the ride.