If you look at the coffeescript or hogan preprocessors you will see how we include javascript as an embedded resource and execute it using either jurassic or a wrapper around IE's javascript engine.
From here it is pretty easy to implement your own IJavaScriptMinifier
You can then register it globally using the following somewhere in App_Start:
Bundle.ConfigureDefaults().UseMinifierForJs(new MyUglifyMinifier());
This is not included in the framework assembly because both techniques bring pretty heavy dependencies. If you want to start an issue on github to see if there is a lot of demand for this I can keep an eye on it - it may make sense to have different minification packages available on NuGet similar to what we have for preprocessors.