- Conditionally render out the contents of the linked Component in your Page Template Design.
This'll let you add JS on a per-page basis without having to create duplicate templates (and without having to duplicate the JS itself).
The simplest way to add JS to your header in your Tridion implementation is to keep JS out of the Tridion CM and deal with it purely on the presentation side. To do this, simply render the path to the file on your presentation server. This means keeping your JS bundled along with other presentation side code.