I know that this is not the answer you are looking for, but I usually process it with a build script, either in Bash or in Rake (yes, Rake, great for creating PHP projects) that compiles, integrates and compresses my .coffee files for production. During development, I use coffee -w to compile .coffee files on the fly.
You can automate this by adding a post-commit to Git or Subversion afterwards, if you like.
You must upgrade the Mark Story Asset Compress plugin to compile on the go.
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