To prevent that, just put this line at the top of your component entry point file (component.php):
In Joomla 2.5
JHTML::_('behavior.mootools'); // this code make sure that mootools loads first your code here
In Joomla 3 and later
JHtml::_('behavior.framework');// this code make sure that mootools loads first your code here
Now in your jQuery plugin, return the jquery handler.
var jQ = jQuery.noConflict(); // now use jQ instead of $ symbol your code here
or just the below code
jQuery.noConflict(); // this will keep using the $ symbol your code here
Now everything is set, you can use both liabrary in your code.