At first you do not check for existence of a second element of an array, but check it's truth.
You can rewrite it like this:

foreach my $entry ($result->all_entries()) {
    foreach ( $entry->attributes() ) {
        my $ra = [ $entry->get_value($_) ];
        $r->{$entry->dn()}->{$_} = @$ra > 1 ? $ra : $ra->[0];
    }
}
[download]

Update: lexical $r renamed to $ra