There are ways to remove the markup using regexes. Try this:

$page = "my ##Media Wiki [text|here]";
%wordcount;
@words = split /(\s*|#|\[|\||\]|@|$|!|.|,)/ $page;
foreach $word (@words)  {
  $wordcount{$word}++ if $word =~ /\w/;
}
foreach $word (keys %wordcount)  {
  print "$word\t$wordcount{$word}\n";
}
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