GitHub's response neither confirms nor denies any part of the story. It does say the founder's wife will no longer be allowed in the office, but that is not an admission of wrongdoing nor of her ever having been in the office.
Edit: The only thing this response proves is that GitHub is taking these allegations seriously, which hopefully means there will be more information after they have time to investigate. Try not to jump to the many other conclusions already posted in HN comments.