With regards to the FAQ section in your post...
If I'm interpreting what you're saying correctly, then the idea of necromancy and undead is only considered evil because of the associations created by the various religions of the world, and the assumption of an alignment restriction on a primal energy (which has always seemed completely off-piste to me too!). Therefore, in a culture which disdains gods and dogmatic principle, using scientific understanding and the 'soul' of their people as their divine guidance instead, the proliferation of undead people throughout society would be more akin to elders and priests than any sort of unholy creature. They're quite the opposite, and I like this.
You may wanna check this out, it's possibly a wee bit overpowered, but would be a MASSIVE boon to a world like this one.
Your 'Strange Thought' isn't so strange at all, it makes perfect sense actually. You may want to look at the Kalashtar in RoE, they have a racial awareness (almost like a psionic substrate) which may be a good source of inspiration for this 'Gestalt Socio-Entity'.
As far as Utopia/Dystopia, reality is in the eyes of my Beholder
Perspective is everything.