I don't understand. Do think Reeva went into the bathroom, opened the bathroom window and went into the toilet knowing an intruder was in there or not realising one was in there, or did an intruder come in there after she was already in the loo after having opened the window ?
I have not heard OP say he shouted "burglar in the bathroom, get out of my house", or "Reeva call the police there is a burglar in the bathroom", so how would Reeva know the intruder OP was shouting about was in the bathroom so as to render her unable to phone the police or call out to OP for fear of being heard, as she heard OP getting nearer shouting for her to call the police.
And had she known a burglar was in the bathroom, according to some, ready to shoot an occupier at first sight, then why would she be standing near the door and not crouched in the corner behind the toilet, or to the left of the toilet pressed against the left wall and a much more auto protect position than standing free in front of a door.
Curiously according to SA crime statistics surprisingly few people are killed during house break-ins and of those some are the thieves.