I have no inside knowledge, but I'm betting that the ARM version of Windows will strictly run .net user applications. (There's already precedence for this with Windows Phone.)
Microsoft already tried to support Windows on two different architectures (x86 and Alpha) and failed when application developers never bothered porting to Alpha. They're not about to repeat that.
.NET stuff is not native code. It's CLR bytecode, interpreted much the same way Java bytecode is. Some runtime environments do JITing, when the bytecode gets translated to native instructions.
Microsoft already tried to support Windows on two different architectures (x86 and Alpha) and failed when application developers never bothered porting to Alpha. They're not about to repeat that.