Compare $new_uri with d()->name and not d()->uri in the Site Rename Check.

platform/migrate.provision.inc

@@ -31,7 +31,7 @@ function drush_provision_drupal_pre_provision_migrate($platform, $new_uri = NULL
   drush_set_option('old_platform', d()->platform->name);
 
   // If we are renaming the site, pick this up early.
-  if (!is_null($new_uri) && ($new_uri != d()->uri)) {
+  if (!is_null($new_uri) && ($new_uri != d()->name)) {
     drush_set_option('target_name', $new_uri);
   }
   else {
@@ -81,7 +81,7 @@ function drush_provision_drupal_provision_migrate($platform, $new_uri = NULL) {
 
   $options['uri'] = d()->uri;
 
-  if (!is_null($new_uri) && ($new_uri != d()->uri)) {
+  if (!is_null($new_uri) && ($new_uri != d()->name)) {
     $options = d()->options;
     $options['uri'] = ltrim($new_uri, '@');
     $hash_name = drush_get_option('#name') ? '#name' : 'name';
@@ -137,7 +137,7 @@ function drush_provision_drupal_post_provision_migrate($platform, $new_uri = NUL
 
 
 
-  if (!is_null($new_uri) && ($new_uri != d()->uri)) {
+  if (!is_null($new_uri) && ($new_uri != d()->name)) {
     // remove the existing alias
     $config = new Provision_Config_Drushrc_Alias(d()->name);
     $config->unlink();