Source Maps (SMAPs) are the solution, ie. files that map between the source language and the target representation. Google’s Closure compiler can generate SMAP files for it’s minified Javascript files, although currently the only tool that can read the SMAP files is the Closure Inspector, a Firebug extension. 

Both the Mozilla and the WebKit projects have started work on supporting SMAPs in their debugging features. 

This should remove the last concern many people have about using CoffeeScript.