Is feeling fear and confusion when speaking with a superior at work, with the intention of pleasing him or showing good conduct, considered Shirk (associating partners with Allah)? And what should be done to repent from that, and does that necessitate leaving the job?

This fear is natural and occurs to some people. It does not affect faith as long as one believes that no one can harm or benefit except Allah. Do not preoccupy yourself with these intrusive thoughts (waswas); your faith is firmly established with certainty. Neither of the two interpretations you mentioned for your fear is considered disbelief (kufr). Disbelief only occurs when one embraces it wholeheartedly and finds tranquility in it, not merely through passing thoughts or an act of disbelief not intended to abandon Islam. Leave these satanic whispers, continue with your work, and you must supplicate and turn away from those thoughts.