Disabling Mootools in Joomla 1.5 was actually pretty simple. All you need to to is add the following to your template above your head tag:

getHeadData();
    $headers['scripts'] = array();
    $this->setHeadData($headers);

    // make sure to eliminate any of the following
    //JHTML::_('behavior.framework', true);
    //JHTML::_('behavior.mootools', true);
?>

In Joomla 1.6 this can remain the same if you adjust a tiny bit of Joomla internals. Specifically we need to modify the setHeadData() function in joomla16/libraries/joomla/document/html/html.php (around line 116).

// original version
$this->_scripts = (isset($data['scripts']) && !empty($data['scripts'])) ?
                  $data['scripts'] : $this->_scripts;

// updated version ( !empty() replaced with is_arrray() )
$this->_scripts = (isset($data['scripts']) && is_array($data['scripts'])) ?
                  $data['scripts'] : $this->_scripts;

What this does is allow Joomla to accept an empty value for $headers['scripts'] where it would previously reject it.

Let me know if you have any questions.

Happy coding!