Yeah, all the good extensions are taken -- .cof and .cfs are already other things as well. None of the tooling in the compiler cares about what extension you use: you can call it .coffeescript if you'd like. I'm going to stick to .cs for the parallel to .js for the time being.
I think the biggest issue is that it makes it hard for programming environments to pick the right syntax coloring. There may also be problems selecting the MIME type when serving the file.
So if you have to use a conflicting file extension, you probably want to use one that isn't already associated with a major programming language or web file type.