You seem to think that I'm suggesting that Pistorius didn't do it, or that his story is plausible, or that his initial story about thinking it was a burglar was quick thinking. I'm saying none of these things.
I'm saying that his story isn't implausible because it necessitates the burglar having a dump, because it doesn't. It is implausible for other reasons.
Maybe story form will help:
Doctor [bursting into appartment]: What's going on here mun - I heard some bangs.
Pistorius: I shot my girlfriend through the toilet door.
Doctor: Why did you do that mun?
Pistorius: I thought she was a burglar.
Doctor: You thought she was a burglar taking a dump in your appartment? That hardly sounds very likely.
Pistorius: No, you utter nincompoop. I thought she was a burglar climbing through the window.
Doctor: Oh right. But still, your story sounds implausible for other reasons - for example, as Getsme says, why didn't you check on her. Plus the whole street heard her screaming.
Pistorius: Yeah, I don't have a leg to stand on do I?
Doctor: Hahahaha. Nice one. But yeah, you're screwed.