Re: Ignoring "Negative" Ki
I have a hunch you didn't look away out of fear, but rather out of embarrassment and regret at the position you have put him into. A position I believe you did not intend to put him in.
Big lesson here is not where to look.
The phrase "discretion is the better part of valor" comes to mind. Bringing that into a martial sense, the personal and discreet reporting of the incident to a supervisor you can trust to do likewise. Minimizing public exposure of the incident, not just for the janitor, leaves your employer the greatest amount of discretion to exercise in any event. Whether they see and/or use this discretion is another matter entirely.
Yea, none of this seems related to aikido, self defense, or "munen mushin" until you think of the possible end results. The potential for this man to lose his job over the incident is far more dangerous to you than whatever may have transpired in the office had you not been there.
In the opposite direction the janitor may look on you with respect for your adept handling of a tricky situation ; at best a misunderstanding, and at worst just a poor decision on his part.
I mean, what if like yourself, he was just looking for a quiet place for a nap?
Naturally had the janitor been violent, or some clear and harmful motive discovered, he forfeits consideration before his employer, and/or you individually.
The proper excercise of discretion would allow you to gauge how your response would affect this person's life. Hmmm, sounds a lot more like it relates to aikido, huh?