The sample you mention says XNA isn't supported. It doesn't say C# isn't supported.
Since C# isn't a scripting language it needs to be compiled before it can run. Folks that have used C# as a scripting language in a C++ game engine have used Code Access Security to keep the script from doing bad things. However, Metro apps all have to pass certification which means that code must be compiled up front. So if you are creating C# scripts and can compile those before hand I would think you could make it work in Metro. But you definitely can't have .cs files on the machine where users could create mods to your game by changing the .cs file and have your game compile them on the fly.
If you can precompile the scripts then you can actually make your scripts WinRT components.
There are 4 requirements for WinRT components.
(Note: These 4 requirements are only needed on the public types and members in your component)
API signatures must use only Windows Runtime types
Structs can only have public data fields
All types must be sealed
Only supports system provided generic types.
VS has a project you can use to create a WinRT component.
I'm still getting my head around all things Metro, so take my information with a grain of salt. Hopefully someone from Microsoft can provide better information.
Assuming you can precompile your scripts and ship them as precompiled WinRT components you should be fine. If that doesn't fit with the game you are making, then it may be that you need to stick to a Desktop game.