If I understand what you are doing, and the problem you are having, the first thing I’d try is to add your the_content filter with a large priority number so that it runs late, and hopefully after the other formatting filters.
add_filter('the_content','your_callback',100);
If that doesn’t do it you may have to remove and reorder some some filters.
If this is a page and you can edit the template for that page, you could also run get_the_content, apply the content filters to it, then append your form before you echo.
$content = get_the_content();
$content = apply_filters('the_content',$content);
$content = $content.$your_form;
echo $content;