https://github.com/PocketMine/PocketMine-MP/blob/master/src/pocketmine/inventory/CraftingManager.php Since $recipesLookup is protected, you may need to use reflections to do that. But it is highly discouraged because that means the plugin may break in future versions. Therefore, basically, it is not possible to unregister a recipe. The proper way to disallow use of a certain recipe is to handle CraftItemEvent.
Because plugins shouldn't do unrecoverable things. Well, you just don't need to do that. There is CraftItemEvent.