// Unset all but the #tree property, so that taxonomy is no longer a fieldset.
foreach (array_keys(element_properties($form['taxonomy'])) as $property) {
 if ($property != '#tree') {
   unset($form['taxonomy'][$property]);
 }
}

// Give the taxonomy an explicity weight to position it in the form.
// Of course, you may need to give other elements weights too....
$form['taxonomy']['weight'] = 3;