Many people mention Microsoft's past history as reasons for worrying about this. However, I disagree. I don't think this would be bad because it's Microsoft.
I think it would be bad because GitHub wouldn't be a generally independent entity, with no business interests besides making a product good enough that people will pay for it anymore. Currently, GitHub doesn't really have any incentive to care what tools and platform you are using, or where you deploy your code. To the contrary, they want to appeal to the widest audience possible.
This would all change if owned by Microsoft. GitHubs role would then instead likely instead be to channel users into other Microsoft products and services, especially Azure. Instead of functionality that benefits everyone independent of platform, it will be in their interest to add features that only benefit users of the Microsoft ecosystem. Azure CI, deploy to Azure, .NET integration, LinkedIn integration. I don't think this is the kind of platform most FOSS projects would want to use, certainly not me.
This is what I was thinking also (though you articulated it much better than I would have).
A large company doesn't make an acquisition like this without a business incentive. For them, it's driving people to their products. Maybe making the tooling in github for interacting with microsoft-y products a little bit better. Maybe adding whatever licenses microsoft likes to the front of the default licenses you can pick from when you create a new repo. Things generated by their editors going into your .gitignore by default.
I don't see any reason they'd acquire github and then entirely leave it alone.
I think it would be bad because GitHub wouldn't be a generally independent entity, with no business interests besides making a product good enough that people will pay for it anymore. Currently, GitHub doesn't really have any incentive to care what tools and platform you are using, or where you deploy your code. To the contrary, they want to appeal to the widest audience possible.
This would all change if owned by Microsoft. GitHubs role would then instead likely instead be to channel users into other Microsoft products and services, especially Azure. Instead of functionality that benefits everyone independent of platform, it will be in their interest to add features that only benefit users of the Microsoft ecosystem. Azure CI, deploy to Azure, .NET integration, LinkedIn integration. I don't think this is the kind of platform most FOSS projects would want to use, certainly not me.