There is no way to turn off the Taxonomy module's term listing pages in Drupal 5 or 6 (I haven't tried in version 7). One way to disable them is to add the following to the top of settings.php:

# Return a 410 Gone response if viewing a taxonomy term search page.
# These can be found at /taxonomy/term/123...
if (preg_match("/^taxonomy\/t/", $_GET['q'])) {
  header("HTTP/1.0 410 Gone");
  print '
Gone
';
  print '
The requested page has been removed permanently.
';
  die();
}

You can also redirect to a 404 page instead if you prefer.

if (preg_match("/^taxonomy\/t/", $_GET['q'])) {
  header("HTTP/1.0 404 Not Found");
  header("Location: http://example.com/error404");
  die();
}