1. Edit file qa-theme/<your-theme>/qa-theme.php
2. Add or merge the following function:
public function head_custom() {
parent::head_custom();
echo <<<HTML
<script>
your code here
</script>
HTML;
}
Anyway, as I said, your hosting provider should tell you why you can not upload <script> tags to their server. It's not really a Q2A issue.