Why do you use the @col_1 and @col_2 arrays? Also it's more efficient to store just undefs in the hashes and then use exists():

$sql = "SELECT col_2 FROM theTable WHERE col_1 = $value_1";
$sth = $dbh->prepare($sql) or die("Could not prepare!" . $dbh->errstr)
+;
$sth->execute() or die("Could not execute 1!" . $dbh->errstr);
while ($data = $sth->fetchrow_array()) {
    $union{$data} = undef;
}
$sql = "SELECT col_2 FROM theTable WHERE col_1 = $value_2";
$sth = $dbh->prepare($sql) or die("Could not prepare!" . $dbh->errstr)
+;
$sth->execute() or die("Could not execute 2!" . $dbh->errstr);
while ($data = $sth->fetchrow_array()) {
    $isect{$data} = undef if exists $union{$data};
}

@isect = keys %isect;
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