Another option is to use NoNumber's extension called ReReplacer. With this extension, you can keep mtupgrade enabled ( needed for things like Kunena and other fun mootools scripts ) but you can have ReReplacer remove the call to the mtupgrade plugin only for the Virtuemart component.
It's really simple to do. Just install the rereplacer component. Check out the source code on your virtuemart page, copy the code that looks like this:
<script type="text/javascript" src="/yadda/yadda/plugins/system/mtupgrade/mootools.js"></script>
then create a new rereplacer rule, paste that script in the first box and leave the second box blank. Make sure that you have the "everywhere" option selected, just take a look at rereplacer, it's great ( as are all of Peter's extensions ).