It's not super-clean but having put the script in your Scripts folder for the theme you can use Layout.cshtml to control which scripts get loaded and you can use Request.Path to control the pages they show up on. For example, if you had a control that
only appears on the home page of your site you could put this in Layout.cshtml in your theme:
if (Request.Path == "/")
This at least eliminates any need to put script tags into the body of any page and you have full control over Head, Footer, UseCdn etc..