Your question got me thinking, because I'm going to be adding a separate nav menu to my footer. I started by changing this code in the functions.php file:
/* Activate native wordpress navigation menu and register a menu location */
add_theme_support('nav_menus');
register_nav_menu('avia', THEMENAME.' Main Menu');
to this:
/* Activate native wordpress navigation menu and register a menu location */
register_nav_menus(array('avia' => THEMENAME.' Main Menu', 'my_footer_menu' => 'Footer Menu'));
since my footer menu is brilliantly named "Footer Menu" and the add_theme_support call isn't necessary in either version. I then added this code:
<?php
wp_nav_menu( array( container => false, 'menu' => 'Footer Menu' ) );
?>
to the footer.php file right below the last footer widget. It eliminates the megaWrapper DIV but still leaves the avia_mega class on the menu's UL container. Still, I think that answers your question. Hope this helps.