Microsoft's new future is to be a cross-platform vendor for developers. I see absolutely zero incompatibility between Github and Microsoft and a need to shut it down. I think the Satya's Microsoft is smart enough not to ruin it.
Now MSFT just needs something along the lines of Jira to replace the dog’s breakfast that is VSTS Agile project management tooling. I don’t suppose the folks in Redmond are looking to acquire Atlassian next...?
Most of the discussio here is just centered around Microsofts goodwill and trustworthiness, mostly ignoring that MS wouldn't make this investment without a solid plan and path to profitability.
That doesn't have to be bad per se, I guess there are a lot of options like integrating Github well with Azure and providing alternatives to AWS CodeCommit / pipelines, ...