I'm not so worried about it. Microsoft has been much friendlier to open source in the last 5 years. They open-sourced .NET Core, VS Code, TypeScript, etc. They have a community edition of Visual Studio. They are one of the most prolific contributors on GitHub already.
They already have their own competing solution, Visual Studio Team Services that uses Git, so they're not buying tech. (I honestly think VSTS is nicer tool than GitHub. Plus they offer a free tier that has private repos unlike GH).
Some have speculated that the move is so that they can push people to Azure, which is the real moneymaker. I would think that they wouldn't want to alienate developers away from that by mucking the product they all love.