I think MS has finally learnt the lesson that Nintendo taught when they brought that poison pill that was Rare.
You can buy a company, but you can't buy the people in the company.
That is why Nintendo rarely buys out a company and is happy to let developers go when it is time. Now we can collectively stop asking Nintendo to use that "War chest" because it isn't going to happen.
Either way, it is MS's lost and al Bungie's gain. From a PR stand point alone, MS has effectively lost their golden developer. Even though they have held on to the IP, an IP a game is not. MS could milk the same engine and gameplay, but without the controlling vision behind it, it just wouldn't be the same. I doubt Bungie does any of that imparting wisdom stuff that Miyamoto does.
Bungie wins. They are already rich, potentially rich enough to self publish, even if not, got the kudo's to get almost any publisher to do it for them. They are not longer slaves to MS. They can work on what ever dream project they want. Corporate deadlines and milestones are gone. They are no longer constrained by the demographic of the console they work with.