As of now, JavaScript files can be loaded in the theme by using the javascripts and javascripts_footer options.
However, loading a JavaScript Module proved to be a bit troublesome, since I couldn't find a proper place to include it in the theme, and finally decided to override the constructor through the course_renderer in order to call the AMD Module that was needed for the theme.
Is there a proper - and less crude - way to include modules the same way as simple scripts are included? I couldn't find any, and also didn't find an issue about this in the tracker.
If there's no such thing, then what are your thoughts about adding a new feature to the theme config to enable this?