The problem here is probably one of the processing procedures. I assume your PHP code is evaluated after rendering the head block. Although your code successfully updates an instance of the head block class, this happens after the result has been generated from that instance.
addJs() XML, . , ifnotconfig, .
, script , .
<?php
class My_Module_Helper_Class extends Mage_Core_Helper_Abstract
{
public function getJsBasedOnConfig()
{
if (Mage::getStoreConfigFlag('mymodule/settings/enable')) {
return 'path-to-file/file1.js';
}
else {
return 'path-to-file/file2.js';
}
}
}
XML:
<?xml version="1.0"?>
<layout>
<default>
<reference name="head">
<action method="addJs">
<file helper="classgroup/class/getJsBasedOnConfig" />
</action>
</reference>
</default>
</layout>