In my opinion, there's a distinction that needs to be made between a "mystical natural order" vs. simple manipulation of the environment. I assumed that since I'm imagining a world with magical necromancy, that there would be some sort of overarching magical order. I also disagree with your assessment of unnatural. In what way is building a shelter purely unnatural? It's not explicitly a human function to do so. Beavers, birds, termites, and wasps build shelters. Bonobos in captivity have been observed using firewood and matches to create fire to cook food. Most of the medicines we have discovered derive from plant based sources that already have antibiotics and antiseptics. Is it only unnatural when humans do it? Or by your logic are those natural flora and fauna also behaving unnaturally?
The Butterfly effect analogy doesn't hold water with me because inaction is a form of action. I think it's absurd to suggest that every action has the potential to be immoral based on consequences we can't possibly extrapolate. It's about what seems to be a reasonable conclusion. For example if you were to say, break a butterfly free of a spider's web; that could in theory have incredibly profound implications. It could be the spider was running out of energy and that butterfly was it last hope. In freeing it, you doomed the spider to death. That in effect removed its progeny from the gene pool. It could also be that spider contained a genetic mutation that made it's venom toxic to specifically cancer cells. This venom could have been studied and perfected into a reliable and mass producible cure for cancer. In freeing that butterfly, you condemned countless to die at the ravages of cancer. Is that really a consequence ANYONE would reasonably predict? Now let's say I were to decide to get completely staggeringly drunk and drive home in my tank. On the way, I hit a car and kill three people. That's a much different story. There are any number of people who will tell you that getting into a tank and driving it drunk is an awful idea and that a reasonable and predictable consequence is that you'd hit someone and kill them. If you are a con artist preying on parents with sick children selling them placebos in place of real medication, it is reasonable to assume a child might die as a result of a stupid parent believing that some angel came out of nowhere and sold them "medication" at a price though while high, was something they could afford.
That brings me to the mystical natural order especially concerning life and death. In many pieces of literature, messing with that order has catastrophic consequences. Even if one were to ignore all that, the fact is that people wouldn't actually know how far reaching tampering with that could be. It seems reasonable to assume however, that if this order is responsible for the souls and animation of every person alive, that breaking or tampering with it could have some serious consequences. It's purely conjecture, but I feel it's a cautious educated hypothesis based on the sheer number of people and creatures dependent on it.
That's precisely why I tried to draw a distinction between necromancy that "returns life to the dead" vs animation via an electric current or arcane energy that effectively works as a "meat puppet". One case tampers with something for which the consequences are unknown and potentially terrible. The other is essentially creating a marionette of flesh, which while potentially distasteful and grotesque, is not immoral. In the case of raising non-sentient creatures, it's not the act itself that is immoral, it's what you do with those meat puppets.