It would be great if they added this and I +1ed the new work item added.
However I worked around this in an odd way by using a chirp.config like this:
<!-- Chirpy automatically removes the last '.debug' so this ensures it stays.
Also must include 'min' even if it isn't minified to work with ScriptManager automatic debug settings.
<FileGroup Name="woo.min.debug.debug.js" Minify="False">
<!-- Chirpy automatically adds .min to the end when minifying so the name below really is 'woo.min.js' -->
<FileGroup Name="woo.js" Minify="True">
Saving this XML as "woo.chirp.config", Chirpy will output a "woo.min.debug.js" and "woo.min.js". Then your script reference points to woo.min.js. It is odd because the woo.min.debug.js isn't actually minified, but it still works.
A nice side-effect is that you can combine several js files into a single one by adding more File sections above.
But globally, it would be great to have this functionality built-in.