I made some changes to printGroups to use same "seen trick". Won't print the same $groupData{$group}{line} twice. Could be some flaw here, but this is a quick way that looks like it produces the desired output.

my %seen; ###

sub printGroups {
    my ($groups, %groupData) = @_;

    for my $group (sort @$groups) {
        next if !exists $groupData{$group};

        if (!$seen{$groupData{$group}{line}}++) ###
        {                                       ###
           print $groupData{$group}{line};
           print @{$groupData{$group}{data}} if $groupData{$group}{dat
+a};
           printGroups($groupData{$group}{groups}, %groupData)
               if exists $groupData{$group}{groups};
        }                                       ###
    }
}
 =prints
access-list INSIDE_IN extended permit tcp object-group DNS-CLIENT obje
+ct-group DNS-SERVER object-group DNS_TCP
object-group network DNS-CLIENT
 group-object PC1_1st
 group-object PC2_1st
object-group network PC1_1st
 network-object host 10.1.1.11
object-group network PC2_1st
 network-object host 10.1.1.12
object-group network DNS-SERVER
 network-object host 10.1.1.5
object-group service DNS_TCP tcp
 port-object eq domain

access-list INSIDE_IN extended permit udp object-group DNS-CLIENT obje
+ct-group DNS-SERVER object-group DNS_UDP
object-group service DNS_UDP udp
 port-object eq domain
=cut
[download]