I, too, had once thought Samuel Allen's second wife, Mary was an Alden. When I had attempted to apply for membership in the Alden Kindred Society, I was turned down because they do not believe she was an Alden. I agree strongly.
I believe that Samuel's second wife was Mary Pratt, daughter of Matthew and Sarah (Hunt) Pratt of Weymouth. Both of Mary's parents were said to have been afflicted by an illness that made them deaf. Perhaps she was put under the guardianship of Joseph and Mary (Simmons) Alden, and was, thus, thought by some to have been one of their daughters? Even still, she may have been married first to an Alden?
Naming patterns in the subsequent Allen family seem to suggest that Mary was, indeed, born Mary Pratt.