Since times are tough no one is in there pushing around store managers ~ everybody will check out anything you want to buy.
Like Mr. Hussein across the way says, the prohibition is on eating pork, not on handling it.
I suspect the other poster from NY is correct ~ the clerk (probably a young woman) is underage for ringing up beer and wine.
The other half of the equation is common here too ~ they'll take a newbie and put up a sign "NO MEAT SALES" ~ which has to do with breaking in the cashier ~ didn't they used to call that ON THE JOB TRAINING?
First the drygoods with barcodes, then the items sold by weight, and that'd include fresh meat and veggies.
Next week she'll be handling pork snouts without a whimper.
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.