Do you mean debugging third party closed source code? If not just debug normally like we have done decades (and even in web world few years using these "source maps"). If it cannot be done today it will be then when it's main stream.

Probably not, once tooling is in place. Running an implementation of the .NET platform would make it possible to attach standard .NET tools to the application running in the browser. (Once it was implemented in the .NET interpreter, of course.) That would give you a much nicer debugging environment than you'd normally get in a JavaScript application.