Bungie wanted independence and with it higher royalties. The issue of Halo ownership was never in doubt. That's MicroSoft's. So they came to an amicable arrangement, where Bungie would work on ODST and Reach, almost certainly for higher royalties than before, and perhaps in the future they will continue to work together the way that independent studio Insomniac works with Sony. The gain for MS was that they had no studio who could deliver Halo quality in as timely a fashion as Bungie could deliver ODST and Reach, and it meant Bungie wouldn't be developing games for competitors and for PS3. MS is staffing up internally now to create a future Halo, and that carries significant risk (and expense, compared to the well oiled machine which is Bungie).
I don't see this as anything at all like the ATVI-IW situation, which is very far from amicable and could lead to a loss of talent while Modern Warfare 3 is still unconfirmed, as well as that talent working directly for the competition.