I would do it in a different way - js should be external, obviously, but why not take full advantage of the fact that you have an MVC framework that's perfectly suited to handle all of your javascript magic?
Here's my recipe for Javscript (and CSS) goodness with CI:
Grab a copy of Minify - if you don't know it already, your life will be better. Not in a "Love at first sight / I just discovered jQuery / xkcd / unit testing" kind of way, but at least in a "Dude, prepared statements eradicate SQL injection" kind of way.
Second, create a CI controller that encapsulates Minify (shouldn't be too hard, just remember to set the correct HTTP header and pass the parameters on)
Optionally activate caching to make everything run blazingly fast (Minify has caching built in, but if you're already caching your CI content, you might as well use the same method here.
Optionally define some groups for Minify, to make script loading even nicer
Optionally add the baseurl and siteurl variables (and whatever other values you may need) to the javascript output
And presto, you should now be able to load your scripts by calling the Minify-wrapper:
<script type="text/javascript" src="/min/g=js"></script>
It's crazy fast, it's gzipped, takes just one request rather than many, it gives you full CI control over your scripts, and it even makes your source code cleaner.
Oh, and if you want to be extra nice to your source-code-peeping visitors, you could automatically add something like this to the output:
// Javascript compressed using Minify by Ryan Grove and Steve Clay
// (http://code.google.com/p/minify/)
// Human-readable source files:
// http://www.yourdomain.com/js/core_functions.js
// http://www.yourdomain.com/js/interface.js
// http://www.yourdomain.com/js/newsticker.js
// http://www.yourdomain.com/js/more_magic.js
(...)
At least that's what I do.