Simple Magento script, that deletes all non admin store associated prices ... basically we will keep only the default prices values and will delete all website associated price values.

delete-non-admin-prices.php

<?php
/**
 * @author      MagePsycho <info@magepsycho.com>
 * @author      ceckoslab  <ceckoslab@gmail.com>
 * @website     http://www.magepsycho.com
 * @website     http://ceckoslab.com
 */
$mageFilename = 'app/Mage.php';
require_once $mageFilename;
Mage::setIsDeveloperMode(true);
ini_set('display_errors', 1);
umask(0);
Mage::app('admin');
Mage::register('isSecureArea', 1);
Mage::app()->setCurrentStore(Mage_Core_Model_App::ADMIN_STORE_ID);

set_time_limit(0);
ini_set('memory_limit','1024M');

/***************** UTILITY FUNCTIONS ********************/
function _getConnection($type = 'core_read') {
    return Mage::getSingleton('core/resource')->getConnection($type);
}

function _getTableName($tableName) {
    return Mage::getSingleton('core/resource')->getTableName($tableName);
}

function _getAttributeId($attribute_code = 'price') {
    $connection = _getConnection('core_read');
    $sql = "SELECT attribute_id
                FROM " . _getTableName('eav_attribute') . "
            WHERE
                entity_type_id = ?
                AND attribute_code = ?";
    $entity_type_id = _getEntityTypeId();
    return $connection->fetchOne($sql, array($entity_type_id, $attribute_code));
}

function _getEntityTypeId($entity_type_code = 'catalog_product') {
    $connection = _getConnection('core_read');
    $sql        = "SELECT entity_type_id FROM " . _getTableName('eav_entity_type') . " WHERE entity_type_code = ?";
    return $connection->fetchOne($sql, array($entity_type_code));
}

function _deleteNonAdminPrices() {
    $connection     = _getConnection('core_write');
    $attributeId    = _getAttributeId();
    $entityTypeId   = _getEntityTypeId();

    $sql = "DELETE FROM " . _getTableName('catalog_product_entity_decimal') . "
            WHERE  attribute_id = ?
            AND entity_type_id = ?
            AND store_id != ?";

    $connection->query($sql, array($attributeId, $entityTypeId, Mage_Core_Model_App::ADMIN_STORE_ID));
}
/***************** UTILITY FUNCTIONS ********************/

$message = '';

try {
    _deleteNonAdminPrices();
    $message =  'Success:: All Non Admin Prices Deleted';

} catch(Exception $e) {
    $message = 'Error:: While Deleting Non Admin Prices: ' . $e->getMessage();
}

echo $message;