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class Ab_CategoryObserver_Model_Observer
{
    public function updateTopMenuJson(Varien_Event_Observer $observer)
    {
      $_helper = Mage::helper('catalog/category');
      $_categories = $_helper->getStoreCategories();
      $recursionLevel = 3; // Add recursion level
      $storeId = 1; // Add your Store ID for which you want to get category tree
      $node = '';
      $categoryTreeData = $this->getCategoryTree($recursionLevel, $storeId);
      $arr = json_encode($this->getCategoryTree(3));
      file_put_contents("cat_node.json", $arr);
    }

    protected function getCategoryTree($recursionLevel, $storeId = 1)
    {
        $parent = Mage::app()->getStore($storeId)->getRootCategoryId();
        $tree = Mage::getResourceModel('catalog/category_tree');
        /* @var $tree Mage_Catalog_Model_Resource_Category_Tree */

        $nodes = $tree->loadNode($parent)
            ->loadChildren($recursionLevel)
            ->getChildren();
        $tree->addCollectionData(null, false, $parent);

        $categoryTreeData = array();
        foreach ($nodes as $node) {
            $categoryTreeData[$node->getData('entity_id')] = $this->getNodeChildrenData($node);
        }

        return $categoryTreeData;
    }

    protected function getNodeChildrenData(Varien_Data_Tree_Node $node)
    {
        $categoryData = array(
          'title' => $node->getData('name'),
          'url'   => $node->getData('url_key'),
          'id'    => $node->getId(),
          // 'mega_menu1'=> $node->getData('mega_menu')
          'mega_menu'=> 'false'
        );

        foreach ($node->getChildren() as $childNode) {
          if (!array_key_exists('children', $categoryData)) {
              $categoryData['mega_menu'] = 'true';
              $categoryData['children'] = array();
          }

            $categoryData['children'][$childNode->getData('entity_id')] = $this->getNodeChildrenData($childNode);
        }
        return $categoryData;
    }
}
1

In getCategoryTree() you can change:

foreach ($nodes as $node) {
    $categoryTreeData[$node->getData('entity_id')] = $this->getNodeChildrenData($node);
}

To:

foreach ($nodes as $node) {
    if ($node->getIsActive()) {
        $categoryTreeData[$node->getData('entity_id')] = $this->getNodeChildrenData($node);
    }
}

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