I heard from a friend that Bungie chose Sony over Microsoft because of the Halo incident. What happened was that Bungie was planning for Halo 4 and Microsoft asked them for a large amount of money (Knowing Microsoft, this was a VERY large amount of money) to produce this game or else they drop the franchise or Bungie would have to give the franchise to another company, so Bungie said screw that, gave it to 343, and went on to Destiny. But like you said about Microsoft taking Bungie under their wing from before and getting them started and all, I think that's where Bungie decided to let Microsoft in on Destiny.