I know it's not so much your own opinion as retelling of an article in Libris Mortis, but allow me to comment on it
None of that explain neither:
existence of Good Liches and Undead Paladins,
nor why Crypt Things and Gravecrawlers are "always Neutral",
nor - for that matter - why Entropic Creature template doesn't affects alignment (easily can be Entropic Paladin - +2 to Con and Cha is handy, and LA +2 isn't too crippling).
Heck, Xeg-Yi Energon is made of Negative Energy, but its alignment is "Always neutral", and neither summoning nor calling it to Material Plane count as [Evil] act
Actually, crafting of Flesh Golem required casting of Animate Dead, so I wouldn't be so sure about the "not powered by negative energy"; and its Berserk SA may do way more damage than extremely vague hazard of "Undead pollution"...
And speaking about that - Elder Evils have a couple of things to say there:
Restless Dead
“Too long have we reveled in our wickedness, too long have we sampled the forbidden—now the gods shun us, sealing the gates to heaven and leaving us lost among the dead.”
When this sign appears, the demarcation between life and death grows ever more blurry. After souls depart, their bodies stir in a wretched existence neither alive nor dead.
The sign of the restless dead first makes itself known by isolated occurrences of zombies and skeletons in the community. As it strengthens, the undead plague increases. Corpses pull themselves free from graves, slaughtering former friends and lovers and swelling their ranks until only the shuffling dead remain.
Effect: In the early stages of this sign, only a few of the dead spontaneously animate. Necromancy magic becomes more efficacious, while healing magic is suppressed. As the sign intensifies, more and more corpses rise, growing stronger all the while.
Details: Atropus (Chapter 2) is associated with this sign. See page 17 for more information.THIS IS THE "UNDEAD POLLUTION"!..Atropus's presence in the sky causes the dead to rise from their graves.
Faint: Necromancy spells and spell-like abilities are cast at +2 caster level. Whenever a living creature dies, a 20% chance exists that it will spontaneously rise as a zombie (MM 265) in 1d4 rounds.
Moderate: As faint, but the chance of spontaneous animation increases to 40%. In addition, the entire campaign setting is affected as if by a desecrate spell (PH 218). Casting consecrate removes this effect in the spell’s area until its duration expires.
Strong: As moderate, but the chance of spontaneous animation increases to 80%. Even creatures that died before this sign manifested begin to rise as skeletons or zombies, depending on the condition of their corpses. In addition, the campaign setting is affected as if by an unhallow spell (PH 297). Casting hallow removes this effect in the spell's area.
All conjuration (healing) spells and similar spell-like abilities are impeded, meaning that a caster must succeed on a Spellcraft check (DC 20 + the level of the spell) or lose the spell or spell slot without effect.
Overwhelming: As strong, but any creature that dies automatically rises as a zombie 1 round after death. Previously dead creatures automatically animate as skeletons or zombies. All undead creatures gain an extra 2 hit points per Hit Die. In addition, they gain turn resistance equal to one-quarter of their Hit Die total (1–7 HD grants +1 turn resistance, 8–15 HD grants +2, 16–23 HD grants +3, and so on). This bonus stacks with any turn resistance a creature already possesses.