Here's one way of doing it:
#!/usr/bin/perl -w
use strict;
chdir('dir1');
open(my $fh, '<', 'list.name') or die("open() failed: $!");
my %all = map { $_ => undef } grep { -d } glob("*");
delete($all{$_}) for ( map { chomp; split(/,/, $_) } <$fh> );
system('rm', '-ir', $_) for (keys(%all));
__END__
format of dir1/list.name:
dir1,dir2,dir3,dir4,etc
dir10,dir11,
dir12,dir_x
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