You could create a php script that did the normal includes and just printed out the result, escaped with javascript

Something like
Code
<?php
ob_start();
// This is where the include code specified in the control panel would go
$out = ob_get_contents();
ob_end_clean();

header('Content-type: text/javascript');
echo "document.write('" . str_replace("'", "\\'", $out) . "');";
?>

You would include this script as such

Code
<script type="text/javascript" src="/script_i_just_made.php"></script>