This is the most definitive link I can find for what is so far a non-story story about Microsoft somehow letting Bungie become independent again.
The official Microsoft response to reports in Jacob Metcalf's blog that allege Bungie is leaving Microsoft was:
There's been no such announcement.
That's the kind of non-denial denial you'd expect from a company that is the subject of so many non-story stories.
Todd Bishop, on his Seattle Intelligencer blog, gets Robbie Bach at Microsoft to comment on that non-denial denial, and ends up getting an explanation of why the non-denial denial exists:
"The problem is, I can't comment one way or another on any of these rumors. Because then, every time you ask me a question about a rumor, I have to comment definitively, and there's times when I don't want to, and times when I do want to. I just don't. You should interpret it that way. You should interpret it as a neutral 'don't.' "
All in all, it seems very likely that people in Bungie might want to, you know, work on a game that isn't Halo, or isn't a shooter, or, God forbid, isn't a Halo shooter. Farming out Halo Wars to Ensemble and Halo Chronicles to Wingnut seemed to me like Microsoft setting up the Halo franchise to continue while Bungie moved on to other things; but perhaps it was just a move to try and maximize the revenue from the Halo property by developing ancillary products with a series of Halo shooters at the center, developed by Bungie.