Howdy :)

What you need to do is replace these lines:

    if ( defined $messages{$id}{to} ) {
        $messages{$id}{to2} = $to;
    } else {    
        $messages{$id}{to} = $to;
    }
[download]

With this:

push @{$messages{$id}{to}}, $to;
[download]

This will give you a HOHOA, and will cater for as many recipients as are found.
Run the following sample code to get an idea.

#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;
my %messages;

while (my $line = <DATA>) {
    if ($line =~ /relay=127\.0\.0\.1/) {
        my ($id, $to, $status) = (split /\s+/, $line, 10)[5,6,9];
        chop($id);
        $to =~ s/to=<(.*?)>,/$1/;
        push @{$messages{$id}{to}}, $to;
    }
}

print Dumper(\%messages) and exit;

__DATA__
Nov 16 10:28:51 smtp3 postfix/smtpd[17709]: connect from mailserver.ou
+rdomain.gov.au[168.x.x.x]
Nov 16 10:28:51 smtp3 postfix/smtpd[17709]: 66AE820809D: client=mailse
+rver.ourdomain.gov.au[[168.x.x.x]
Nov 16 10:28:51 smtp3 postfix/cleanup[19600]: 66AE820809D: message-id=
+<56FE9AD99802CE47AF144E03064331D501F42840@mailserver.gov.au>
Nov 16 10:28:51 smtp3 postfix/qmgr[9315]: 66AE820809D: from=<Terry.Pus
+er@ourdomain.com>, size=11466, nrcpt=2 (queue active)
Nov 16 10:28:51 smtp3 postfix/smtpd[19599]: connect from localhost.loc
+aldomain[127.0.0.1]
Nov 16 10:28:51 smtp3 postfix/smtpd[17709]: disconnect from mailserver
+.ourdomain.gov.au[168.132.65.6]
Nov 16 10:28:51 smtp3 postfix/smtpd[19599]: 883822080A4: client=localh
+ost.localdomain[127.0.0.1]
Nov 16 10:28:51 smtp3 postfix/cleanup[19594]: 883822080A4: message-id=
+<56FE9AD99802CE47AF144E03064331D501F42840@mailserver.ourdomain.gov.au
+>
Nov 16 10:28:51 smtp3 postfix/qmgr[9315]: 883822080A4: from=<Terry.Pus
+er@ourdomain.com>, size=11644, nrcpt=2 (queue active)
Nov 16 10:28:51 smtp3 postfix/smtp[18745]: 66AE820809D: to=<carols@the
+irdomain.com.au>, relay=127.0.0.1[127.0.0.1], delay=0, status=sent (2
+50 Ok: queued as 883822080A4)
Nov 16 10:28:51 smtp3 postfix/smtp[18745]: 66AE820809D: to=<daleb@thei
+rdomain.com.au>, relay=127.0.0.1[127.0.0.1], delay=0, status=sent (25
+0 Ok: queued as 883822080A4)
Nov 16 10:28:51 smtp3 postfix/smtpd[19599]: disconnect from localhost.
+localdomain[127.0.0.1]
Nov 16 10:28:51 smtp3 postfix/qmgr[9315]: 66AE820809D: removed
Nov 16 10:28:52 smtp3 postfix/smtp[19429]: 883822080A4: to=<carols@the
+irdomain.com.au>, relay=mailhost.theirdomain.com.au[203.x.x.x], delay
+=1, status=sent (250 Message queued)
Nov 16 10:28:52 smtp3 postfix/smtp[19429]: 883822080A4: to=<daleb@thei
+rdomain.com.au>, relay=mailhost.theirdomain.com.au[203.x.x.x], delay=
+1, status=sent (250 Message queued)
Nov 16 10:28:52 smtp3 postfix/qmgr[9315]: 883822080A4: removed
[download]

Hope this helps,
Darren :)