I think the real answer here, is to have the plugin author load scripts properly using wp_enqueue_script().
Or, you could change the theme enqueue code to output jquery to the header by changing to this (not great for performance reasons, but relatively simple):
wp_enqueue_script( 'jquery', get_template_directory_uri() . '/js/jquery/jquery.min.js', array(), '1.0.0', false );
Or, you could rewrite the plugin code so that it uses the enqueue process.