Прервать выполнение скрипта и вывести запрос можно строкой:

exit($query_sel);

Вот код:

<form name="edit_fk" action="edit_fk_su.php" method="post" target="main">
<?php

if ($_POST['kaf'] && $_POST['thema'])

$basename=$_POST['kaf'];
$id_thema= $_POST['thema'];
$id_fk=$_POST['fk'];
include "config.php";

echo '<br>';
$quer = "select * from DISCIPLINE where DISC = $_POST[discip] order by DISC";
    $res4 = mysql_query($quer);
    list($DISC, $D_NASME)=mysql_fetch_row($res4);
    echo "<p>&nbsp; Дисциплина:&nbsp;&nbsp;";
    echo "<input type=text name=D_NASME size=100 value=\"".$D_NASME."\">";
    echo '<br>';
echo '<br>';
    echo "&nbsp; Тема:&nbsp;&nbsp;";
            $query_sel = "select * from GLAVA where ID_GLAV=$_POST[thema]";
            $res_sel = mysql_query($query_sel);
            list($id_glav, $id_disc, $N_glav, $GL_NAME)=@mysql_fetch_row($res_sel);
            echo "<input type=text name=thema size=100 value=\"".$GL_NAME."\">";
            echo '<br>';
echo '<br>';

$select=mysql_query("select * from active_fk WHERE ID_GLAV=".(int)$id_thema.";"); 
  if(mysql_num_rows($select))while($mass=mysql_fetch_array($select)){
    $active[$mass['ID_FK']]=1;
  }
$select=mysql_query("select * from form_kont" );
  while($mass=mysql_fetch_array($select)){
     echo "<label>".$mass[NAZV_FK]."</label>"; 
    echo "<input name='check[".$mass[ID_FK]."]' type='checkbox' value='1'";
   // echo "<input name='check[".$mass[ID_FK]."]' type='hidden' value='1'";
     if($active[$mass['ID_FK']])echo('checked="checked"');
     echo "/><br>";  //все ок-значения считывает
   }
   echo "<br>";

if(isset($_POST[$active[$mass['ID_FK']]]) && strlen($checkbox[1])> 0)
{
    $active[$mass['ID_FK']]=1;
  }
//проблема здесь

echo "<input type=hidden name=kaf value=\"".$_POST['kaf']."\">";
echo "<input type=hidden name=discip value=\"".$_POST['discip']."\">";
echo "<input type=hidden name=thema value=\"".$_POST['thema']."\">";
echo "<input type=hidden name=fk value=\"".$_POST['fk']."\">";
echo '<input name="insert" type="submit" value="Добавить" align="center">';

?>
</form>