Well, Pistorius knew exactly where to shoot. Any shots into that small cubicle would hit their target. Anyone on the inside of that cubicle shooting out would have no idea at all where to point the gun, particularly if they were an intruder entering the flat for the first time, and obviously with no knowledge of the layout. The idea that Pistorius thought his life in danger from shots from within a toilet behind a closed door is not tenable.
Any intruder who would have entered the cubicle would have seen the layout of the bathroom before entering it, having come through the window in the main bathroom area. Granted, someone inside the cubicle wouldn't know exactly where Pistorius was standing, but given that he was apparently almost constantly shouting at both the intruder and towards his bedroom, there would be some clue as to his position.
Pistorius was also on his stumps, so probably not moving too swiftly.