MooTools 1.2 is finally in Joomla!
For upgrade installs, this plugin is not enabled by default.
If you had followed my previous method, then you simply need to remove the code you added to your template's index.php, and enable the new Mootools Upgrade plugin through the Joomla Extension manager.
I have run into at least one situation where the new Mootools was required, but Joomla wasn't including it on certain pages. To force Joomla to included MooTools throughout your entire template, simply add the following code to your index.php: