I have my suspicions that this story will prove to be NOT true. I have looked on M&S' website at their staff terms and conditions and there is nothing to confirm this story.
http://corporate.marksandspencer.com/documents/specific/howwedobusiness/our_people/employeehandbook
Both the Mail and Telegraph stories are remarkably similar, including a customer who was alledgedly refused by a muslim checkout girl but who wished to remain anonymous. Both reports are structured the same as if they are from the same source. The reports do not have confirmation from a senior M&S manager.
I would not be surprised if the alledged M&S directive (if it exists) may say muslim workers can be exempted from working on the shopfloor handling meat and alcohol, but that would not include serving customers. And would not allow staff to refuse to serve customers.
If this was Call my Bluff, I am holding a "False" card.