Using jQuery inline code

Hello,
I use your plugin on new site and it add this code to the footer of page:

<script type="text/javascript">
jQuery(document).ready(function ($) {
$("ul.nav-menu").not(":has(li)").hide().closest('div').hide();
});
</script>

I use Autoptimize plugin to combine all JavaScript files to one. But your code need jQuery to be linked in before. Is it possible to include this code in separate file or rewrite this code to vanilla JavaScript?

Thank you
Thomas