There have been rumors forever about how how difficult the Daily Show is to work on because Jon Stewart is a perfectionist type that goes hard, can be really sensitive to criticism and has really high expectations from his staff. I want to say he's had similar problems with a couple female staff members as well. Some people can deal with that environment, some people take it personally, so I have zero doubt that the scene happened just like Wyatt Cenac said it happened.
Having said that, Wyatt sounds like a bytch that expected his boss to be a father-figure. Making fun of Herman Cain isn't racist, it's what anyone with half a functioning brain would do, just like making fun of Trump. Telling your liberal comedian boss, who is known for his silly voices and has (like it or not) spoken out about honestly about race in this country more than anyone else in the mainstream, that he sounds like he's Kingfish in a meeting full of people and while he's already getting shyt on by the real enemy isn't going to end well. At all. Ever. That whole "crying like a middle school girl on the baseball field" because he got told to fukk off visual doesn't do him any favors either.
So yeah, they're both wrong. Stewart cannot take criticism and I've never seen Wyatt be funny outside of the Daily Show - his stand-up was a borderline therapy session.