Yes, that is the problem; someone else's religion inconvenienced him, because he will be inconvenienced every time he's served by her.
A sick employee? That might happen once. Running out? Well, the store is going to do everything in its power to make sure that doesn't happen again.
Ms. JW chef will always refuse to serve him.
The store realizes this is a problem and they try to cover it up by saying it was a misunderstanding. But, they know it's a serious faux pas because it's insulting.
A customer hears that they won't be served because of a person's religious convictions that class the item he has asked to eat as sinful. That's an insult. You're being served an item that has been deemed so disgusting by an employee that he can't even touch it to serve you.
Insulting the customer is not a good way to do business. That's why the customer was offended and that's why the store explained it away as a mistake.