MooTool Upgrade or Turn Off

I notice that this template uses the older version of mootools in joomla. I have a MooFlow viewer that uses mootools 1.2. It works fine with the basic joomla templates however with this one it clashes. Is their any elegant way to turn off the MooTools related functions? I went in and found the head.php and commented out the joomla mootools behavior but that didn't seem to help. Any help would be grateful.

Joomla! 1.5.* officially supports MooTools 1.1.* - MooTools 1.2.* will be supported in Joomla! 1.6. That's why our templates scripts are based on MooTools 1.1.*

mootools.js file can be included by some extensions if you're using it on your website.

Yea but I'm trying to turn it off. After a bunch of hacking I figured out the area's that was causing the conflict. I totally understand your reasoning behind implementing it using joomla's mootools. I'm going to eventually have it only turn off in certain pages but just to push forward I commented out the lines of code that was causing problems. Thanks anyway