There are a couple game development companies that have had complex relationships with Microsoft. I'm thinking of Bungie, which originated Halo and later split off from Microsoft to become independent again, only to eventually sign with Activision (Sony) for the production of their MMO Destiny.
Then of course there's the interesting ride that Lionhead Studio went on with Microsoft and the release of Fable. Ultimately, it was Microsoft's decision to close Lionhead due to the lack of success of the Fable follow-ups. I don't necessarily see that happening with Obsidian, since they are much broader and diverse in their development capabilities than Lionhead was. It does make me wonder if Obsidian will be able to pursue some projects independent of the Microsoft bean-counters. They seem very capable of having many irons in the fire at once.
"A world is supported by four things: The learning of the wise, the justice of the great, the prayers of the righteous, the valor of the brave, but all of these are as nothing without a ruler who knows the art of ruling - Make that the science of your tradition."
The Reverend Mother Gaius Helen Mohiam from the novel Dune