Lots of reasons. If someone were employed by, say, the Gestapo then it's pretty clear you would want to discriminate against them.
Can we stick to discrimination against the employees of legal employers in one's own state that one recognizes as legitimate and one is not in active rebellion against?
It's certainly not a good excuse to go ignoring important lessons in history. Nazi Germany is one of the better examples of why "just doing my job" is not a valid excuse for anything.