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GitHub will retain its developer-first ethos, operate independently, and remain an open platform. Together, the two companies will work together to empower developers to achieve more at every stage of the development lifecycle, accelerate enterprise use of GitHub, and bring Microsoft’s developer tools and services to new audiences.
Microsoft has realised that software business is different and GitHub is how it's different.
It's only different in that Microsoft got a pretty sweet deal by having to pay only pennies on the dollar or nothing at all for all of the "FREE" work being done in 26 or some odd million public repositories
The code in public repos is all as free (or not!) as it already was