Since she had no other injuries she obviously wasn't assaulted. So your theory is wrong.
And in any case, the idea that someone would murder to cover up a minor assault is somewhat improbable.
If this was her first overnighter, it is plausible that he woke up to noises in the bathroom and basically forgot that she was there. If he was paranoid about home invasions that would be a possibility.
He didn't wak up to noises in the bathroom. Per his affidavit, he was on the balcony getting a fan when he heard the noises from the bathroom. And he very well remmebered she was in his apartment, since in his affidavit he claims his goal was to protect himself and her. Yet when he went to get his gun from under the bed, he never even checked whether she was in that bed.