Magento – How to Remove Associated Products from Configurable Product

I had the same issue and here is what I've used. It's a 'quick and dirty' script that works with the database directly, so back up you DB before trying it. Also add the table prefix if you have one.

$resource = Mage::getSingleton('core/resource');
$attributes = array('image', 'thumbnail', 'small_image');
$connection = $resource->getConnection('core_write');
$collection = Mage::getModel('catalog/product')->getCollection()
    ->addAttributeToSelect($attributes)
    ->addAttributeToFilter('type_id', 'configurable')
    ->setOrder('sku', 'ASC');

foreach($collection as $product){
    //$product->load($product->getId());//not sure if this is needed
    $simpleProductsIds = $product->getTypeInstance()->getUsedProductIds();
    $q = "SELECT * FROM catalog_product_entity_media_gallery WHERE entity_id = {$product->getId()}";
    $result = $connection->query($q)->fetchAll();
    foreach ($result as $row){
        $q = "SELECT * FROM catalog_product_entity_media_gallery_value where value_id = {$row['value_id']}";
        $valueResult = $connection->query($q)->fetchAll();
        foreach ($simpleProductsIds as $id){
            $q = "INSERT INTO catalog_product_entity_media_gallery SET
                attribute_id= {$row['attribute_id']},
                entity_id = {$id},
                value = '{$row['value']}'
            ";
            $connection->query($q);
            $lastInsert = $connection->lastInsertId();
            foreach ($valueResult as $val){
                $q = "INSERT INTO catalog_product_entity_media_gallery_value SET
                    value_id = {$lastInsert},
                    store_id = {$val['store_id']},
                    label = '{$val['label']}',
                    position = {$val['position']},
                    disabled = {$val['disabled']}
                ";
                $connection->query($q);
            }
        }
    }
    //update media images
    $data = array();
    foreach ($attributes as $attribute){
        $data[$attribute] = $product->getData($attribute);
    }
    Mage::getSingleton('catalog/product_action')
        ->updateAttributes($simpleProductsIds, $data, 0);
    echo "Done with product: ".$product->getId()."<br />";
}

It took about 20 seconds for 80 configurable products and about 400 simple products associated to configurable.
If you have 20k products I don't think it's a good idea to iterate the product collection like I did. You can use Mage::getSingleton('core/resource_iterator'). More about it here.

When you have some configurable products created on the basis of that attribute you can't delete the attribute. But if you want to really delete that attribute, you have to delete the products first.
You will not find any hacky method for it. These attributes are saved in eav attribute table and products just get its id (attribute_id) to relate. so if you delete the attribute, you will face errors like "something is being load non-object..." etc, and you may even not be able to edit that product at backend nor it will load at frontend. so be cautious before committing such things on live.