Overwrite or Replace code in WP_Footer

Since you ruled out remove_action there is only one way you can do it. And you’ve guessed it: preg_repalce, substr mixture but with a little help and PHP DOM

add_action('wp_footer', 'my_start_footer_ob', 1);
function my_start_footer_ob() {
    ob_start("my_end_footer_ob_callback");
}

add_action('wp_footer', 'my_end_footer_ob', 1000);
function my_end_footer_ob() {
    ob_end_flush();
}

function my_end_footer_ob_callback($buffer) {
    // remove what you need from he buffer

    return $buffer;
}

Within my_end_footer_ob_callback you edit the $buffer to your needs. The $buffer parameters should have all the contents of the footer after all actions and filters have been call to action. If it does not simply edit 1000 to a bigger number so that my_end_footer_ob is called last.

Now, I do not know what HTML contents that action produces but you can use pre_replace or a sequence of substrs to remove it.

If you want to use PHP DOM do it like this:

function my_end_footer_ob_callback($buffer) {
    // remove what you need from he buffer

    $doc = new DOMDocument;
    $doc->loadHTML($buffer);

    $docElem = $doc->getElementById("theID");

    if($docElem !== NULL) // if it exists
        $docElem->parentNode->removeChild($docElem);

    return $doc->getElementsByTagName('body')->firstChild->nodeValue;
}

Tell me if this works for you.