You don't have to use the C# features of Godot. You can still use GDScript to code your game in, or GDNative with any extending language like D, Go, or Rust, so long as you find bindings for them. I wouldn't worry about Microsoft being owed favors, I'd worry more about actual licensing, and if it wasn't for Microsoft (or so I suspect) Mono would still not be as openly licensed as it is now[0].
Note how Microsoft was mentioned for their license change (why would that be if Microsoft had nothing to do with the change, wondering if buying out Xamarin gave them power over making Mono more open), and it was announced at the annual big Microsoft event no less. I'm all for yelling at Microsoft when they screw up, but they're doing good things with .NET and C#.
I notice the post reveals ms has funded the project now. I hope Godot doesn't owe ms any favours..