Like this?

#! perl -slw
use strict;
use Data::Dump qw[ pp ];

sub uniq{ my %h; undef @h{ @_ }; keys %h };

my @pairs = map[ split ], split ', ', 'A B, B C, C D';;

my @uniq = uniq( map @$_, @pairs );

my %mat; @{ $mat{ $_ } }{ @uniq } = (0) x @uniq for @uniq;

$mat{ $_->[0] }{ $_->[1] } = $mat{ $_->[1] }{ $_->[0] } = 1
    for @pairs;

pp \%mat;

__END__
c:\test>880739
{
  A => { A => 0, B => 1, C => 0, D => 0 },
  B => { A => 1, B => 0, C => 1, D => 0 },
  C => { A => 0, B => 1, C => 0, D => 1 },
  D => { A => 0, B => 0, C => 1, D => 0 },
}
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