The article claims GitHub said that the wife would "work from home". Why would a company say that a non-employee would "work from home". Why would a company allow a non-employee to get into the office that much?

This sounds a lot worse and blatant than just shoulder surfing at home.

GitHub uses campfire, but HipChat does not give any way for a account owners/admins to read personal 1-1 chat logs.

Hipchat user/admin; agreed. I don't have access to 1 on 1 chat logs and I prefer it that way.

Same exact situation for me, definitely don't want to be reading anyone else's chats or for there to be any concern that someone might be listening in.