On the whole, though, I don’t think CoffeeScript adds quite enough benefit to outweigh the costs It's not clear what are those costs? The --watch mode bug? Or the generated JS which is perhaps less a complaint about CoffeeScript, and more a warning about versioning and standardising all components of a project.? Or the author's trouble with indentation rules?
I've had to read this article too many times to figure out, but it sounds like the author is looking for a framework like backbone. Author used the wrong "tool" for his main problem. A language doesn't really help avoid spaghetti code, as author concedes: It is still possible that I may find a return to plain Javascript sufficiently painful that I’ll stick with Coffee.