You might not be familiar with how modern computer graphics work. Objects and textures are loaded into the GPU and managed with an API like OpenGL and shader programs written in languages such as GLSL. Java, in this case, serves as the engine that ties everything together and runs the core game logic.

Microsoft rewrote it because they're not a Java shop. Microsoft Games Studio not only uses C#, but their mission is to increase adoption throughout the industry as it feeds into Microsoft's ecosystem. Microsoft is about developer mindshare.

C# and Java are incredibly similar languages. They're almost indistinguishable. Pointing to C# as if it's substantially different from Java makes me think you've never used either.