Add custom email field input validation to check for unique email addresses for each field. You can add this to a site specific plugin.

ee_add_unique_email_validation.php

<?php
//* Please do NOT include the opening php tag, except of course if you're starting with a blank file

function ee_add_unique_email_validation(){
  wp_add_inline_script( 
    'single_page_checkout',
    'jQuery( document ).ready(function($) {
      $(".ee-reg-qstn-email").addClass("unique");
        $.validator.addMethod("unique", function(value, element) {
        var parentForm = $(element).closest("form");
        var timeRepeated = 0;
        if (value != "") {
          $(parentForm.find(":text")).each(function () {
          if ($(this).val() === value) {
              timeRepeated++;
          }
      });
    }
    return timeRepeated === 1 || timeRepeated === 0;
    }, "* Duplicate! Please use a unique email address");
    } );'
  );
}
add_action( 'wp_enqueue_scripts', 'ee_add_unique_email_validation', 60 );