Microsoft is a great sugar dady for Bungie, but at the same time they essentially won't let Bungie do anything but Halo. I think Bungie has said on more than one occassion they're getting tired of the pressure of Halo and living up to expectations of sequels that quite frankly couldn't deliver past the first instalment.
But without MS they'd just be another leaf in the breeze and could easily sucuumb to the same woes of Silicon Knights.