Index: wp-includes/ms-functions.php
===================================================================
--- wp-includes/ms-functions.php	(revision 35739)
+++ wp-includes/ms-functions.php	(working copy)
@@ -786,10 +786,7 @@
 	}
 
 	// Send email with activation link.
-	if ( !is_subdomain_install() || get_current_site()->id != 1 )
-		$activate_url = network_site_url("wp-activate.php?key=$key");
-	else
-		$activate_url = "http://{$domain}{$path}wp-activate.php?key=$key"; // @todo use *_url() API
+	$activate_url = network_site_url("wp-activate.php?key=$key");
 
 	$activate_url = esc_url($activate_url);
 	$admin_email = get_site_option( 'admin_email' );