We don't know if it's absolutely true or not, only that it's possible.
Jefferson did try to seduce the wife of a friend, so we can't assume he was above having relations with one of his slaves.
We might also consider the ethics of picking some Jefferson relative or other and putting the blame on him. It may have been tough enough being one of Jefferson's relatives and living in the great man's shadow without being made his fall guy two centuries later.
What's significant about the Barton controversy, though, isn't Sally Hemings, it's Barton's attempt to turn Jefferson into an orthodox Christian believer. While Jefferson may not have been the complete infidel that New England Federalist ministers feared, he was far from orthodox Christianity.