"1. You're using Negative Energy
As shown in Manual of the Planes, the Negative Energy Plane is Neutral. Negative Energy does not mean Unholy."
That's not exactly true. While the plane has no "evil" descriptor, that is only relevant to the fact that it doesn't actively target Good people, while ignoring Evil people. It's neutral to that axis, since it hurts EVERYONE. It's not "evil" really, but it IS destructive. To the extreme. And usually, utilizing destructive energy is also destructive.
Negative energy is basically Bad (since things that hurt are bad, and things that heal are good). Since D&D is a very black-and-white world, Bad generally equals Evil, although that's not written anywhere. It's also true that hurting things can be either Good or Evil depending on the intent, so in certain conditions using Negative energy isn't a Bad thing. That's why not all uses of Negative energy is considered Evil. There ARE however some uses of it that are. And in the D&D world (which again is cut-and-dry) those spells are labeled as [Evil].
Now, if you desired to make a game with more shades of grey (like our own modern world) then you could relax or throw out all together the restrictions of Good and Evil. However, you would also face some redesign on any ability that relies on alignment. If there is no clear distiction between Good and Evil (the condition that you would have if you threw out those descriptors) then there would also be no clear distiction between Good and Evil people. By the same logic you've used (it's basically the intent and use of the spell, not the spell that makes it [Evil]) then that would also apply to people. You can be a basically Bad person and do Good things, therefore you aren't "Evil". Alignments would be practically useless, since it's the current state of thought of a character that dictates it's alignment, not a proscribed set of beliefs. So people could be "Evil" one moment, and "Good" the next. (Just as casting "Animate Dead" could be used both for "Good" and "Evil".) So it's possible to blend these things into a less cut-and-dry world, it would just take some work on your part.
Another option is you could just decide that the denizens of your world really don't concern themselves with what happens to a body once the soul has passed away. To them, the body is just a shell that has no significance without the soul to inhabit it, therefore using the body afterward wouldn't be desecration.
Last, you could always just make it not [Evil] because you don't want it to be. Rule 0 always takes president!