There is a difference, do we judge the quests objectively -- based strictly on merit -- or subjectively -- that is, taking into account the actual mechanics of playing the game, with all the bugs, quirks, etc.
Objectively, powering up Mephala's Ebony Blade is definitely the evilest deed you can imagine, mass betrayal and murder of those who trust you.
Eating someone's corpse seems almost beyond reproach by comparison.
But subjectively, you don't really need to betray even a single friend, you can, for example, kill Jaree-Ra (which is probably a good deed, actually) and power the Blade from his corpse 10 times, raising him over and over.
In my game, I have no qualms about most Daedric quests, but some Dark Brotherhood missions are very difficult for me from the moral standpoint.