Now, I have seen separate tobacco & alcohol checkouts, but never for groceries. These were legal requirements, not the wishes of the checker.
It is fundamentally bad business practice to cater to the employee rather than the customer. The religious restrictions of the checker are irrelevant to the customer. If you inconvenience & aggravate customers, they will shop elsewhere. Smart businesses don't do that.
We didn't get a picture of the sign ~ and that means ~ this may be an analysis of what was going on as a new cashier with an hajib (scarf) is trained.
Maybe someone could follow-up with that store and see what the story is.