If you're searching for an exact match you might as well use a hash:

my $commonWords = {}; # Make commonWords a ref to an empty hash

...

while (my $line = <>)
{
  chomp($line);
  $commonWords->{$line} = 1;
}

...

if ($CkDiscardCommonwords eq 1)
{
  return(0) if exists $commonWords->{$term};
}
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