Technically that's a hard case to try. Gotta imagine there's hardly any actual witnesses to what happened, and there's zero DNA evidence. She waited to come forward as well which, while completely understandable, makes it even easier for the defense to poke holes in the story.
Plus she had a working relationship with him as well, which left her even more open to shitty claims such as "Durrr, if he raped you why did you still let him be your boss? NOT SOMETHING A RAPE VICTIM WOULD DO DURRRR" and that kinda logic just lodges itself in the mind of idiot jurors as well.
Sad result but not surprising at all.