How to pass information by reference from a hook to Feeds?
The hook hook_feeds_before_update() doesn't support skip items. You could use the hook hook_feeds_presave() instead. Set $entity->feeds_item->skip to TRUE if you want to skip saving the entity. See feeds.api.php for an example.

You could also use the hook hook_feeds_after_parse() to remove items from the list to be imported. The items are in $result->items. This hook is invoked before processing happens, so at this point it is still unknown to which entities the items will be imported (you have no entity ids). Feeds Tamper uses this hook to modify the data to be imported.