Show Home Link In wp_nav_menu but only on primary menu

function my_page_menu_args( $args ) {
    if($args['theme_location'] === 'primary')
        $args['show_home'] = true;
    return $args;
}
add_filter( 'wp_page_menu_args', 'my_page_menu_args' );

The $args array also contains the theme location, so you can filter on that.