Can you insert Craft variables into SCSS files and have a plugin generate CSS?
I did the port of AutoMin to Craft, and I don't think what you want to do is possible with it. Maybe if you were somehow able to write a new file to disk, with the variables defined in it, and then feed that into the AutoMin, it could work. But seems like a pretty complicated solution.

I'm not sure exactly what you're trying to achieve, but in previous projects where I've let the user control colors and fonts on certain objects, I've just done it with pure CSS. If I wanted to let the client define the link color, I'd just do something like this in :

&lt;style type="text/css"&gt;
    a { color: {{ myGlobal.linkColor }} }
&lt;/style&gt;


And then not define the link color in my stylesheet. 

But this is maybe too simplistic for what you're trying to do? :)