I strongly suspect that most people will write their entire game in an engines default language. Especially in this case where the much advertised best alternative (C#) gives you a warning on startup about not being production ready.
Yes, C# is probably integrated due to its success in Unity, but it's a sane choice. I would argue more so than GDScript. C# has better performance, tooling, support, not to mention an existing userbase of people who already know (and I'm sure many of whom like) the language.
Ignoring C#, they cannot be breaking their API for writing native code. I'm not sure if it was a one time thing, or if it will continue going into future releases, but they absolutely need to have stability if they want people to use their engine long term.