I have heard the same theory from some black friends of mine. They told me that the black community here is dead set certain that she was the "woman scorned" and mad because he married a white lady.
I'm not sure that they had an affair though. My former college roommate was working for Justice Thomas at the EEOC. She testified on his behalf during the hearings, and IIRC she was asked directly about their relationship and didn't say word one about an affair. The impression I got (and I do remember her testimony because I turned on the TV and said, "OMG! It's my roommate!") was that she was interested but he was not. And BTW my roommate would not tell a lie - I know 'cause I lived with her for 3 years and she is dead set honest.
Thomas, who was head of the Office of Equal Opportunity, should not have been involved in any way with a subordinate. Should. Not. So if the affair rumor was true, he got what he deserved.
If, as your roommate believed, there was no affair but an emotional "jilting", it sounds like Thomas did not handle a personnel problem effectively. Nevertheless, I believe the harassment took place pretty much as she described it, and her shock that the head of OEO could speak this way to a woman subordinate stuck in her craw. Being emotionally interested in someone is not an invitation to hear about "pubic hairs" and "Long Dong Silver" at work.