Most sources I've seen on the subject flip-flop over whether undead are inherently evil or not, despite negative energy itself being neutral and a perfectly natural part of nature.
The flippant but short answer is because author of the game decided it was Evil (with a capital "E", as the Rules of the universe decree it to so). And said author was influenced by the general view of necromancy as black magick, or the blackest of black magick.
Any other answer is hand waving at best and fan wanking at worst, a justification for how the world works.
But I'll play ball. Why are undead evil?
You hit on most of the arguments, but present them very one-sided. So let's start by looking at those.
1) Desecration of a body. This is ridiculous because people in D&D have solid proof for the afterlife and therefore death holds absolutely no mystery or suspense for them. Therefore they shouldn't treat their dead the same way we in the real world do, because they know for a fact that corpses are nothing more than hunks of rotting meat that retains impressions of the memories of the soul that used to own it, but the actual soul has moved on to the afterlife and has no connection to the body other than for purposes of resurrection.
People in a D&D world have solid proof for an afterlife, which also means they have solid proof their bodies are the creation of god(s) and they have tangible knowledge of the existence of the soul. So animating the dead is desecrating the creation of a god and being rude to the vessel of a soul that is not yours.
There's no reason they wouldn't want to treat bodies with respect. We treat bodies with respect because we
believe they had a soul. Why would knowledge negate that?
2) Negative energy is evil, positive energy is good. For one thing, enough positive energy will make you explode. For another thing, without negative energy nothing would ever be able to die and make way for new things to exist. (or else, why would these two planes even exist?) Positive and negative energy represent life and death, respectively. But because death is scary, people assume it is therefore evil and then we get things like various grim reaper monsters that simply carry out the natural workings of the cosmos receiving "evil" as their alignment.
This is an iffy one. Presentation of the Negative Elemental Plane is spotty at best.
The argument that without negative energy things would not be able to die is... questionable. Death is arguably the absence of positive energy not the presence of negative energy. And the NEP typically represents "unlife" more than "death". It's anti-life.
3) Undead are unnatural/It prevents resurrection magic. How is raising someone from the dead any less unnatural than raising them as a zombie? In fact, resurrection is MORE unnatural because it actually drags the soul from the afterlife and places it back in the body. Scratch that, raising it as an undead is just as natural as letting it rot, since both reanimation and the natural cycle of decay are caused by negative energy (otherwise, why would the plane exist?). Which is really inconsistent that the force responsible for natural rot also preserves undead bodies, but we'll ignore that little self-contradiction.
This is the big one.
First, arguably decay is caused by the positive plane as microorganisms are alive. But that's likely a side topic on how death and decay works in a magical world...
Second, resurrection magic has been presented as "unnatural" on more than one occasion and more than one Death god has been anti-resurrection. But, at its worst, raising the dead just delays the natural order. And most resurrection magic explicitly cannot be used on somewhat natural deaths (old age). And you cannot raise an unwilling creature, so it's not forcing someone to come back (no dragging back a soul like in Buffy).
Raising the undead is a continual violation of the natural order. It's a continual slight against nature.
4) Animating a zombie/skeleton/whatever tortures the soul inside it. For one thing, most undead explicitly do not have souls, as stated by any spells that can manipulate souls. The only undead that retain their souls are things like liches and vampires, whereas others are either mindless hunks of meat/bone or developed a simple intelligence to replace their original soul. For those latter undead, their souls are enjoying the afterlife, and nowhere near the reanimated corpse. Even for intelligent undead, their souls aren't being tortured, they were either evil to begin with or had an alignment shift (or were/stayed good for some reason), which still isn't soul torture and is usually reversible.
You overlook ghosts and the like. Spectral undead
are tortured souls being denied a peaceful afterlife (or escaping their just punishment).
And while liches are not tortured, they're very much the exception. Not everyone chooses to be a vampire: most vampire spawn are victims, potentially still with a soul that is slowly being corrupted and tainted with years of unnatural hunger. The same could be said for ghouls.
The reasons are also not exclusive. A vampire is both #3 and 4, which makes it worse than just raising the dead or torturing a soul.
An unmentioned reason is that many undead infect others with undeath spreading their curse to innocents. Wraith, specters, shadows, ghouls, and mohrg create spawn.
