Microsoft and Bungie ARE splitting. Sort of. According to the press release, it looks like Bungie's going private and independent. Microsoft will maintain a minority stake as well as ownership of the Halo franchise. The split also appears to have been contingent on a long-term development contract between Microsoft and Bungie. The terms of that deal haven't been disclosed.
Presumably, this means that a bunch of Bungie executives got together and bought back at least 51% of the company from Microsoft. They haven't said how large of a minority stake Microsoft maintains, but it can't be more than 49%. In a way, this makes sense; the deal seems to have been designed to keep Bungie, as much as possible, an XBox-exclusive developer. Between the minority interest of unknown size and the binding long-term contract, it's unlikely that Bungie will be rushing to develop for the PS3 or the Wii any time soon. Also, the rumblings heard from Bungie have all been to the effect of the workers disliking the Halo-focus of the company and Microsoft's deadlines. This deal seems like it allows Bungie to become somewhat independent in terms of its management while still maintaining Microsoft's interest in Bungie's creative output.