I can think of several elaborate solutions but I really think that javascript is presentation-level and shouldn't be in your autoload, models, controllers, etc.
You can just use a master view file of some kind with your <head>
and basic HTML requirements:
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title><?php echo $title; ?></title>
<script src="/path/to/jquery.js"></script> <!-- jQuery on every page -->
<!-- alternatively, loop through files in a custom config setting -->
<?php foreach (config_item('default_js') as $src): ?>
<script src="<?php echo $src; ?>"></script
<?php endforeach; ?>
<!-- ... and/or loop through files set in a controller -->
<?php foreach ($js_files as $src): ?>
<script src="<?php echo $src; ?>"></script
<?php endforeach; ?>
</head>
<body>
<header />
<?php echo $content; ?>
<footer />
</body>
</html>
Then just load views like this:
$data['js_files'] = array('draggable.js', 'widgets.js');
$content = $this->load->view('index', $data, TRUE);
$this->load->view('master', array('title' => 'Home', 'content' => $content));
Of course this is just one solution out of millions, but the idea of Codeigniter "autoloading" CSS and Javascript makes no sense, you have to "load" it yourself in one way or another - how you do it is completely up to you.