Do you not think that Ann Farmer may be a possibility then? Misheard by the enumerator? John was a miner, and she's a miner's wife, right age and birthplace. Of course it could be coincidence.
I thought she might be ill long-term, missing from both census, as her mother and sister are living with her husband in 1871, seems odd that she wouldn't be there. However, I've looked through the same infirmary in the 1861 census and can't see her then.
Did they have any children, and do you have her death certificate showing cause of death?
Barbara