Stack Overflow was founded by Joel Spolsky, who is a Microsoft veteran from their era of peak dominance. I suspect it's a passion project of his that he'd like to hang on to, but he's also pragmatic and everything has its price. And it's profitable. I wouldn't be surprised if someone bought it. I can envision synergy between Stack Overflow and GitHub. Satya Nadella seems to really "get it", though, and I don't anticipate any dramatic changes to GitHub, or to Stack Overflow should they take it over.
Spolsky certainly had a strong influence with his ideas and feedback, but I don't think he was ever very directly involved in the project - the main driver was Jeff Atwood. At least that's what I got from listening to the podcast, back in '08.
The idea I got was that he had opinions on how it should work, but that he wasn't involved in the actual development. He's actually written recently on it:
"Jeff started working on the code in April 2008, recruited two other programmers to join him (Geoff and Jarrod, who are still here), and the three of them heroically launched what became Stack Overflow in September 2008."
I'm guessing he was running Fog Creek Software, as its CEO.
StackOverflow has a fairly bad reputation despite its widely perceived usefulness (the community is often seen as toxic and hostile to beginners). Microsoft would have to severely invest into SO's PR and community management. Compare that to GitHub which has gotten over most of its bad press in the past.