Interesting. From what I've read it has never been proved that Jefferson had any relations with Hemings. According to the Jefferson-Hemings Scholars Commission it has never been proved that Jefferson fathered a child by Hemings. The dna tests only show that any of a number male Jefferson relatives could have fathered a child by Hemings.
While the evidence does not totally exonerate T. Jefferson, it also doesn't conclusively show he fathered a child by her.
The problem is that too often, Sally Hemings's status is grossly misrepresented.
She was no ordinary slave. She was in fact Jefferson's sister-in-law, the half-sister of his wife Martha, who died before he ascended to the Presidency. She was nominally a slave because Sally's mother was a half-black slave, but Martha's was a white woman—yet both shared the same father, slave trader John Wayles, who had 17 kids with four different women.
The marital relationships of many of the founders were not always as neat and monogamous as one might suspect (some were). Ben Franklin, for example, never officially married his longtime girlfriend Deborah Read and had a child out of wedlock, William Franklin, a literal Loyalist bastard (though Ben would later adopt William's own illegitimate child Temple). Jefferson's was a perfect example, as he destroyed much of his communication with Martha after she died, making it nearly impossible to deduce the kind of relationship they had.
From what I've gathered, which is admittedly not much, I'm inclined to believe that Jefferson and Hemings were in a sexual relationship. The most telling evidence that suggests that to me is that Hemings's sons
Eston and
Madison acknowledged themselves as Jefferson's sons and Eston gave his children the surname Jefferson. It was not until the 1940s that the connection was forgotten. My firm belief is that it was not an abuse of power as some might have portrayed it, but an example of a close-knit family, and that Jefferson viewed the mostly-white Hemings as a romantic partner far more than a slave.
As for the theory that Jefferson's brothers or cousins may have been the father, I find it far-fetched mainly because Thomas was closest to Hemings, and Occam's razor (the simpliest explanation is usually the right one) would seem to apply.