You don't build applications with logic and complicated function out of HTML and JS. Not today, not tomorrow.
My (and your) 10k, 100k, 200k line C# applications are not writable in JS.
Sure, there is GMail and Node.JS as examples. But thats kind of a niche compared to everything else.
HTML and JS are just going to be another way do to UI, and nothing else. You'll still need to write the C# app and use .NET to do the backend.
HTML/JS will be another option right along with XAML/WPF and SilverLight.