So, Septimus has been reduced to a pile of ash and I have the Oghma Infinium, but when I looted Septimus's corpse, the essence extractor and runed lexicon were available for me to take. I saved before picking up the items, but, the essence extractor is a quest item and cannot be removed from my inventory once I pick it up. Does it have further use in the game, or should I make sure to not pick it up?

Nevermind, it becomes nonessential and not a quest item once the quest is finished. Just tested it.