The second feels the cleaner approach to me as well, but it is not correctly implemented. So I suppose one could argue it is too clever. Alternatively, one could fix it:

sub ripper2b { ## Second implementation, take b
  my $file = $_;
  return unless s/\.(?!$ext)\w+$//i;
  my $priority = "$_.$ext";
  if (-e $priority && !-d $priority) {
    $nom += unlink $file;
  }
}
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• (?!$ext) is zero-width, so (?!$ext)$ is just $. We need to remove the extension as well, whatever it is, so add \w+ to the regex.
• The "." was removed by the substitution, so we need to add it again along with $ext.

If that does not make sense to you, the second implementation is just too clever. Go with the first.