You could do it with an array instead of a hash. You'd have to benchmark it to see whether that makes a noticeable difference. Untested code follows.

chomp(my $line = <IN>);
my @head = split(',', $line);
my @cols;
my $row = 0;
while($line = <IN>) {
  chomp($line);
  my @row = split',', $line;
  $cols[$_][$row] = $row[$_] for 0..$#row;
  $row++;
}
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And if I were really prematurely optimizing this, I'd use 1-@row instead of $#row!