Ironically, Bungie broke off from Microsoft in hopes of more creative freedom, but as per the article, are running an even tighter ship now... Unfortunate.
I think something went wrong with Bungie around the time that Marty parted ways. He also acted out in a way that made it kinda hard to be sympathetic towards him but he seemed to be a big part of what made Bungie Bungie.
Microsoft, Activision, Sony they were never truly independent no studio these days can afford too.
Game development is a mess and a very expensive mess at that, you need a sugar daddy if you would to survive.