In these types of situations, it's usually pretty difficult to come to solid conclusions about the chain of events this early. My initial take?
It's not uncommon for business owners to rely heavily on non-employees for advice, even in the day-to-day operations. Spouses are especially common. What confuses me is that the wife, as portrayed, seems a bit irrational--if not delusional. There's a big difference between even vocal trusted advisors, and the sort of power the wife described herself as having.
So much so that I think there's a third possible interpretation: the quotes are accurate, given by a wife that genuinely believes her statements even though they have no basis in reality. This sort of delusion, in varying degrees, is quite common across the population. We convince ourselves of something--in this case, the wife that she has power in the Github organization--and then attempt to reduce the cognitive dissonance that arrises from the belief and the evidence to the contrary. As time goes on, we try harder and harder to justify those irrational beliefs.
It's entirely possible that there's no truth whatsoever to the wife's words, but that the wife genuinely believed them in spite of it. And that Julie Horvath is entirely accurate in detailing the conversation and the implied hostility she felt from the founder and his wife. So now, not only do you have to determine whether the conversation took place, but also whether the power the wife alleged existed in the first place. Unfortunately for Github, even if the wife never had that power, the wife was still able to contribute to a hostile work environment and that can have significant legal ramifications even though she wasn't an employee.
Friends you go out for drinks with to talk about life and work slowly transform into "spies" who keep you informed of what's happening in the office under the guise of gossip. Curiously taking a peek at an open chat tab on the husband's laptop becomes "access." Commenting on whether you liked a potential hire you met earlier becomes "responsibility over hires." Love for your husband and concern for his work becomes an overprotective desire to shield him from harm.
Given how rapidly Github has grown, the idea that any trusted non-employee, wife or not, would have that sort of power and influence described seems absurd. Hell, for a while it seemed as though they announced a new hire daily. Far too many for one non-employee, no matter how often she went into the office, to have that sort of power. Especially when most were technical positions.
Time will tell, but for now, more information is needed. Anyhow, I suppose I took issue with the phrase "undocumented employee" and ran off on a tangent :). The wife needn't have been an employee at all to have helped cause a shitstorm.