The nephew story is plausible, but doesn't disprove the possibility of Thomas Jefferson's paternity of Sally Hemings's children. It just shows that there is another possibility.
As I like to say, "The existence of Hypothesis B does not disprove Hypothesis A." Contemporaneous documentary evidence supports Hypothesis A, Thomas Jefferson's paternity. John Adams believed it.
He was a fairly old man at the time and a highly accomplished public figure. I can believe this far more of a randy younger male relative who had not yet learned self control than I could of him.