I don’t understand the problem here. Which parts of CoffeeScript require “new syntax” in JavaScript? Isn’t the problem exactly the same if you were using “plain” JavaScript, that at some point in time, if some breaking change occurs in some future version of JavaScript, you would have to change your code? And who says that the CoffeeScript compiler couldn’t be updated to emit proper ES6/ES7/whatever code in the future, just like any compiler (C/C++/Java/…) is able to produce binaries for different platforms or is able to use different language versions.
As far as I understand it, the idea behind CoffeeScript is exactly to have some higher level language that just compiles to “some standard” JS. And if somehow CoffeeScript was abandoned and no one could update the compiler anymore, you still could just compile your CoffeeScript one last time and use the compiled JS in the future.