I think this is a classic problem with companies making the transition from small startup to regular business. Break down the barriers! Flat management! Kill bureaucracy and embrace no-politics DIY organisation!
The article reads like an HR air crash investigation. Nebulous semi-employee with unspecified responsibilities related to a founder? Check. Unclear or absent grievance chain? Check. HR alternately over- and under-involved in disputes with no clear policy? Check. Off-the-record disciplinary meetings? Check. Founder adjudicates his own grievances? Check.
And it seems like every single one of these problems could have been solved by a halfway competent manager. I mean, someone reverting your code because of a personal vendetta? Is that not like, a 5 minute conversation? "Hey, Jo, Dave's being an asshole and reverting my commits for no reason." "Oh, okay, I'll talk to him and make sure it stops."
I read a great article a while back that I unfortunately can't find now, but it talked about a CEO who thought he was having a casual "hey, I'm interested in developing my skills, can you mentor me a bit?" conversation with another exec. A week later the office was ablaze with "so-and-so being groomed as successor" rumours. At a certain point you stop being able to just act like a regular person and have everything turn out fine. Red tape isn't always a straitjacket. Sometimes it's a crash harness.