Microsoft did rewrite the whole game in C++. It's called Bedrock Edition

Why is it scrambled? To keep people from copying it?

Yes. Common practice to hide your code from the user, or potential rivals. I think they've been obfuscating the whole time, even back in Notch days.

It was kinda pointless in this case, and was the reason why mod updates were slow between versions, even for simple mods.

Being written in C++ doesn't keep it from being reverse engineered in exactly the same way. All code can be reversed. It's a little easier with Java because java isn't turned directly into machine-code at compile-time.