Index: wp-admin/includes/plugin.php
===================================================================
--- wp-admin/includes/plugin.php	(revision 15375)
+++ wp-admin/includes/plugin.php	(working copy)
@@ -512,7 +512,9 @@
  * @since unknown
  *
  * @param string|array $plugins Single plugin or list of plugins to deactivate.
- * @param bool $silent Optional, default is false. Prevent calling deactivate hook.
+ * @param bool $silent Optional, default is false. Prevent calling deactivate hook. 
+ *  Used by the updater to internally deactivate plugins, but not notifying them
+ *  of the fact, to prevent unexpected output.
  */
 function deactivate_plugins( $plugins, $silent = false ) {
 	$network_current = get_site_option( 'active_sitewide_plugins', array() );
@@ -539,8 +541,8 @@
 			}
 		}
 
-		//Used by Plugin updater to internally deactivate plugin, however, not to notify plugins of the fact to prevent plugin output.
-		if ( ! $silent ) {
+		// Don't trigger if the plugin will still be active on the current blog
+		if ( !$silent && !( $do_network && in_array( $plugin, $current ) ) ) {
 			do_action( 'deactivate_' . trim( $plugin ) );
 			do_action( 'deactivated_plugin', trim( $plugin ) );
 		}