I've had another look at this too, and although my head's a bit scrambled as a result (!) I agree that the family that Marmaduke has identified in 1841 probably IS Nancy Flather's. There are baptisms for Sarah (2/4/1826), Alfred (10/2/1828), and Thomas (28/3/1830), all at Halifax St John the Baptist, which all tie with the family in the 1841 census, and all give the parents as John and Nancy Mitchell of Northowram, occ. labourer.
At first I considered whether it could be another John and Nancy Mitchell, and there is a Halifax St John marriage 1820 for a John Mitchell in April 1820 to Nancy Bottomley, which might have fitted, but it gives them both as "of Sowerby", which tends to rule out a connection with the Northowram baptisms above.
However, I haven't been able to look at all potential marriages. I suggest it is still possible that the Nancy in 1841 might be a different individual, but the connection with Northowram in the baptisms seems to be a strong pointer that it would be her.