WooCommerce Email Customization

Try filtering the output of that function to remove that column, or set it to an empty string. e.g.

function wpse_120798_item_totals($total_rows, $order) {
    foreach ($total_rows as &$row) {
        unset($row['value']); // or: $row['value'] = '';
    }
    return $total_rows;
}

add_action('woocommerce_email_before_order_table', function() {
    add_filter('woocommerce_get_order_item_totals', 'wpse_120798_item_totals');
});

add_action('woocommerce_email_after_order_table', function() {
    remove_filter('woocommerce_get_order_item_totals', 'wpse_120798_item_totals');
});