In which case the shopkeeper is a vile man who holds prejudices for no reason.
Yes, I would teach him to respect his fellow man. As I would any bigot.
And the rest of your post is assumption and mostly you trying to grasp on to the false feeling that you are correct.
It's alright to be wrong, it's how we learn.
I would accept any reason that wasn't down right idiotic.
To expand:
If the reason was quite valid, I would bring it to the high council and we would try to resolve the problem.
If the reason was valid but, not really worthy of the punishment, I would ignore it and order Imperials to stay away.
If the reason was stupid, I'd advise Imperials to stay away.