Bungie was never it's own entity and they never bought themselves out. Microsoft allowed them to split as long as they made Reach and they also kept equity in Bungie (they actually made money off of Bungie with Destiny even though it was a multiplat)
Bungie's ownership was no different than Lionhead, Turn 10 or any other studio MS owned. They were never their own entity but it was more beneficial for Microsoft to not have to fund anymore of their games (the Halo's were expensive games to make) and still make money off of them (equity in the company). The split was beneficial for Microsoft becaus they were making money off Destiny without ever paying a dime for it vs funding Bungies expensive projects.
Had Microsoft truly wanted to they could of simply closed Bungie down like they did Lionhead, but still kept all the IP's like they did Fable (Playground is making the next Fable) In fact some companies wanted to buy Lionhead but they backed off when Microsoft didn't want to sell the Fable IP. Lionhead had no value outside of it.
Keep in mind, Microsoft didn't even buy Lionhead until 2006, well after the first Fable came out. Closed them down in 2016, still have the Fable IP.
As far as Marathons ownership goes, my guess is Microsoft didn't care, it was an old obscure IP and never saw the light of day, the real value was with Halo which they gave to 343i. Probably let Bungie keep it in exchange for making then happy, having them make Reach and most importantly getting that equity stake in them.
https://www.zdnet.com/article/five-reasons-why-the-bungie-microsoft-split-is-a-smart-move-for-microsoft/
Pretty good read, Microsoft makes money off Bungie to this day because they have an equity in them and pay zero to developing any of their projects. They probably made a killing off of how well Destiny did this gen.
Plus Bungie was always a clusterf*ck of management, if you watch the Halo 1-3 dev videos it was a complete development nightmare, especially Halo 2 with how much they had to cut from the game due to the limitations of the OG Xbox.
There's no such thing as buying themselves back. This isn't ownership by owning a majority of the shares of a company (Bungie and Obsidian were never publicly traded companies and never had stocks to buy) this is a full on acquisition similar to EA buying Bioware, or Microsoft buying Lionhead.
The only way Obsidian would ever stop being part of MIcrosoft is if Microsoft allowed it, in one of the following ways
1) they get closed down like Lionhead, Microsoft would keep TOW IP and whatever else Obsidian makes (Feargus himself owns Pillars) like they kept Fable and give it to someone else like they're giving Fable to Playground
2) Microsoft sells them off, unlikely. Companies offered to buy Lionhead but backed off when Microsoft wouldn't sell the Fable IP. Plus MS isn't hurting for cash
3) They get the Bungie deal and Microsoft LETS them split for economic benefit rather then continue to fund them. Unlikely again because Microsoft 2006 isn't the same as Microsoft 2018. Way different leadership, way different mindset and way different future plans. The biggest reason why Bungie split is because Microsoft wanted them to keep making Halo
Phil Spencer and Matt Booty are adamant on giving the studios they own 100% creative control, they're not going to lock them down to one franchise. In fact Obsidian is apparently working on another project aside TOW and Pillars right now too so they clearly are making new stuff and getting it 100% bank rolled, there's no reason for them to want to split.