It's best to remember the text of
http://www.imperial-library.info/obbooks/black_arts_on_trial.shtml, specifically that :
Necromancy is inherently dangerous. One cannot 'dabble' in it. The simplest spell requires the spilling of blood...
The 'Schools' of magicka are, as we know, artificial constructs, originally formulated by Vanus Galerion to divide and thereby simplify study. They have changed many times throughout the years, but at their heart, every Master knows, they are all linked together. When a student of Conjuration summons a guardian ghost, he is touching on the School of Necromancy. When a student of Enchantment uses a trapped soul, he too may be considered guilty of a Black Art. The School of Mysticism, as I have stated before, has some kinship with Necromancy as well...
... Yes, the Schools are intertwined, but the standard spells of each School have passed the proof of time. We know that a student of Mysticism, properly instructed, will not be permanently harmed by his experience. In many ways, it is a question of extremes - how far we would permit our studies to take us. Necromancy by its nature relies on the practitioner going further into the darkness than is wise, virtually guaranteeing his destruction. It has no place in the Mages Guild.
So the distinction is artificial, but with a bright-line drawn. Simply summoning the undead isn't considered necromancy not because it avoids using magic on the dead or dying -- it aims for these goals -- but because it does not require the drawing of blood or jumping into darkness and has been tested since the days of Galerion, the same as a Shield or elemental Shield spell is a different school than a Resist Damage spell or Summon Armor spell, all of which achieve the same purpose but do so through different underlying means. The Shield spell alters the underlying substance of your body or the air surrounding your body, the Resist Damage spell operates by preemptive healing, and the Summor Armor spell essentially squishes a Daedra into a nice, fun-sized chest plate. In that way, summoning the dead through a Summon Skeleton's underlying mechanics are far more similar to summoning a Daedra -- reach out into others plane, grab a spirit soaked in the magicka constantly spinning past the borders Magnus planned and which separate Nirn from Oblivion, and let them select a form that fits them. Simple, clean, with no harm done to the caster. Meanwhile, even the use of a Necromantic artifact which had already been empowered, such as in
Palla, sent a healthy student into a fever unable to leave his bed for days.
That said, for the sake of sanity, it's best to assume that
Preparation of the Corpse is referring to the construction of intelligent, long-lasting undead. Short-term conjuration spells don't and haven't required the underlying physical components (whether spare ectoplasm or bones), do not leave the underlying corpse behind upon destruction of the spell, or benefit from murder (although they may have that particular aim).
Of course, another theme is that books and statements tend to be at best biased and at worst, wildly incorrect, especially on the matters of popular history or the dark arts, so any explanation that fits the observed reality is supposed to come first in terms of cannon.