Maybe you could just create a new 'Scripts' controller with different actions serving different combinations of compressed JS files. Since MVC is designed with a resource oriented approach, i.e. URLs are now at the center of your programming model, why not define simple URIs for your Javascripts too ?
In your views, for example you could reference your files like this :
<script src="http://your_domain/scripts/all"/>
This would call your 'all' action, resulting in all your compressed script files being sent.
Of course you would need to code the combining and compressing for now, or maybe reuse the Scriptmanager internally, I don't know if it's possible.
This is just an idea though, currently I'm referencing individual javascript files directly in my master pages.