On the contrary, if you argue that the plane of Negative Energy is Evil aligned, then it is you who have moved away from the rules. Just because the plane is entropic does not make it evil.
Now, just to make it abundantly clear, I'm talking about the Undead only within the context of D&D. For the moment, I'm disregarding any existing notions about undead in other media, other RPGs, or even from traditional myths. Further, I'm mostly talking about mindless undead, because as was discussed earlier intelligent undead have the ability to make their own choices about alignment.
Within the context of D&D, there is no reason for any mindless creature to be Evil, unless it is literally made out of Evil (such as outsiders and the like). Mindless creatures operate only on instinct, and thus have no moral agency. They cannot make the distinction between Good and Evil, so they must be Neutral.
Negative energy is not Evil. It is Neutral. This is established fact, because no matter how "evil" sounding the description of the plane is, it does not have the Minor or Major Evil-Dominant planar trait. Casting Inflict Wounds is not an Evil act in and of itself, nor is it even one of the spells granted by the Evil Domain.
If the above points are true, then why are mindless undead "Always Neutral Evil?" They have no moral agency, nor are they animated by an Evil force or have the Evil subtype. The answer to this is because the designer had a preconceived notion about how Skeletons should behave, and aligned them accordingly. It really is as simple as that.
So, this creates two distinct pictures of the world. If you believe that the Negative Energy Plane is Neutral aligned (which is supported by the rules), then you should drop the alignment requirement on Skellies and Zombies. They're as Neutral as golems and other mindless beings that exist only to follow orders, and an uncontrolled skeleton will just sit there and do nothing until someone takes control over it. Furthermore, the [Evil] tag should be dropped from Animate Dead, because you're only creating a harmless puppet, not bringing Evil forth into the world.
If you believe that Skeletons are Evil (which is also supported by the rules), then you should change the Negative Energy Plane to be mildly Evil dominant and add the [Evil] descriptor to any spell that uses negative energy to function. You should also change the Positive Energy Plane to be mildly Good dominant, just for verisimilitude. Under this depiction of the world, an uncontrolled Skeleton will go and attack the most vibrant life-form it can find, whether it's plants, animal, humans, or whatever.
