You just need to change the echo to a link and put the url in the href attribute.
<?php
if (have_rows('file_repeater')) {
while (have_rows('file_repeater')) {
the_row();
$file = get_sub_field('file_upload');
?>
<a href="<?php echo $file['url']; ?>">Download the Document</a>
<?php
}
}
?>
