I am currently working on two projects written predominantly in CoffeeScript, and I completely agree with your original post. It is a mistake to think of CoffeeScript as simply another Javascript, and it is a mistake to make the assumption that people that are comfortable with Javascript will be comfortable within a CoffeeScript project.
CoffeeScript is more than just Javascript with a small sprinkling of syntactic sugar. There is a definite learning curve between Javascript and CoffeeScript. List comprehensions, extended regular expressions, and splats - these are just a few of the things that make up that learning curve. The changes in variable scoping that CoffeeScript makes is another.
I think that perhaps the best practice for publishing a CoffeeScript project should probably be to append a .coffee to the name rather than the usual .js. This would go a long way towards eliminating the kind of misunderstanding that you refer to in your OP.