For good rares that you'll be using a lot, like your starter, Warmaiden, Frozen Banshee, Apothecary, etc., probably using duplicates as skill books makes sense. For a few rares, mostly Coldheart, it may make sense to actually build 2 or even 3 copies of the champion. Fusion rares may also be good to save an extra copy of. But other than that, yeah, they can be used as food.