I've been working on a large project in CoffeeScript for about 9 months now and have never noticed or felt burdened by the translation between JavaScript source line to CoffeeScript source line in debugging. Maybe it's different for others, but the code is so structurally similar that there shouldn't be a major difference. It's not like looking at the assembler output of a C++ program and having to demangle names and deal with compiler-generated labels and jumps etc.; the structure of the program is still the same, it's just the syntax that's really only mildly different.

Of course, though, it comes down to personal preference. Don't want to use CS? Fine! Great! Go hog wild! No one's forcing you to. Me, though? I'll never go back.