^ is what I was about to say.
If you plan on using your manager as a reference for your next job (which is wise) you probably shouldn't go out with a bang.
Though, honestly, I think you're blowing it out of proportion. Even if you were scratching your nuts, it's not like you stood up on the counter, thrust your pelvis outwards, and had a good scratch for the whole place to see.
EDIT: Also, when your next job application asks your reason for leaving previous employer, writing "They thought I was scratching my testicles" on the form probably won't look great.