This bootstrap process doesn't seem correct.

Module bootstrap

<?php
class Sites_Bootstrap extends Zend_Application_Module_Bootstrap
{
    public function initResourceLoader()
    {
        $loader = $this->getResourceLoader();
        $loader->addResourceType('helper', 'helpers', 'Helper');
    }

    protected function _initHelpers()
    {
        Zend_Controller_Action_HelperBroker::addPath(dirname(__FILE__) . DIRECTORY_SEPARATOR . 'helpers', 'Sites_Helper');
    }

    // Using this method, the Action Controller still acts like it can't find
    // a helper by the name of 'search'...
//    protected function _initHelpers()
//    {
//        Zend_Controller_Action_HelperBroker::addHelper(new Sites_Helper_Search());
//    }
}

Sites_FooController

<?php
class Sites_FooController extends Zend_Controller_Action
{
    public function searchAction()
    {
        $this->_helper->search($this->_getParam('query', null), $this->_getParam('page', 1));
        exit;
    }
}