I've gone for an event handler to fix this issue.

class RemoveIndexOnUnpublishEventHandler : ApplicationBase
    {
        public RemoveIndexOnUnpublishEventHandler()
        {
            Document.BeforeUnPublish += new Document.UnPublishEventHandler(Document_BeforeUnPublish);
        }
 
        void Document_BeforeUnPublish(Document sender, umbraco.cms.businesslogic.UnPublishEventArgs e)
        {
            var Nodes = sender.DescendantsAndSelf();
 
            foreach (BaseIndexProvider indexer in ExamineManager.Instance.IndexProviderCollection)
            {
                foreach (var Page in Nodes)
                {
                    indexer.DeleteFromIndex(Page.Id.ToString());
                }
            }
        }
    }

This event handler gets all the children of the page that has been unpublished and removes their entries from the search indexes.

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