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');
});