Magento 1.9 – Is it save to delete all categories associated with products with ‘parent_id’ equals 0?

In a custom module in Magento 1.9 I was associating products to categories using the following method:

public function addProductToCategory($productId, $categoryId)
{
    $category = Mage::getModel('catalog/category')
        ->setStoreId(Mage::app()->getStore()->getId())
        ->load($categoryId);

    $productsInCategory = $category->getProductsPosition();
    $productsInCategory[$productId] = 1;
    $category->setPostedProducts($productsInCategory);
    $category->save();
}

But, as you can see above, I forgot to check if the category actually exists before adding the product to it (using if ($category->getId()) or similar).

This led me to some inconsistency at my database, where some categories were created with blank attributes and parent_id equals to 0 at the table catalog_category_entity (because the $categoryId was invalid).

My question is: can I revert it by selecting all categories associated to at least one product (joining the table catalog_category_entity with catalog_category_product) and deleting all categories with parent_id equals to 0? Something like:

$categoryProductTable = Mage::getSingleton("core/resource")->getTableName("catalog/category_product");
$collection = Mage::getModel("catalog/category")->getCollection();
$collection->getSelect()
    ->join(array('p' => $categoryProductTable), 'p.category_id = e.entity_id')
    ->where("e.parent_id = 0")
    ->group("e.entity_id");

Where the SQL would be:

SELECT `e`.*, `p`.* FROM `catalog_category_entity` AS `e`
INNER JOIN `catalog_category_product` AS `p` ON p.category_id = e.entity_id 
WHERE (`e`.`entity_type_id` = '3') AND (e.parent_id = 0) 
GROUP BY `e`.`entity_id`;

I’ve tested the query above and it seems right, but I’m afraid to be missing something. Any other ideas to solve the problem? Thanks in advance!