The game mechanics saying raising undead is evil. There is no more to argue. It is evil.And yet for all those declarations, there's nothing forcing a character who uses such magic to behave unethically. There is literally nothing that prevents someone from playing a heroic necromancer, nor is such a character required to hurt anybody with his actions or cause any lasting harm. Is such a character good due to his moral outlook and selfless behavior, or evil due to using powers that are defined cosmically as evil?
Sure, it's a disconnect between mechanics and RP.
Nothing says that moving your alignment in a direction forces the behavior of a character to change. But a character that does evil things should behave generally in an evil way.
Now, that doesn't mean that you need to run out and start kicking puppies, but it does mean that you might be scheming in the background how to do something unscrupulously evil.
The disconnect comes from players who want evil powers without the understanding that this should impact how you act. It's a fundamentally evil power that corrupts the users (as evidenced by the fact that it will change your alignment). The character's personalty should change to reflect this. If a GM doesn't enforce this, that's on them.
The game mechanics can't handle everything, especially something like this which would be especially contentious.
Both positive and negative energy can heal or destroy, though.
It is a place of such overwhelming, fecund energy that all non-natives (including some gods) are generally incinerated within seconds of arrival unless appropriate precautions are takenThat's not really helpful; classic "too much of a good thing". Good. Thing.
Meanwhile no amount of negative energy is acceptable to living things.
I think a key thing to understand is there is a fundamental difference between an Animate an Object spell and an Animate Undead spell. In fact, perhaps describe the difference.
Animating an undead fundamentally in core Pathfinder in Golarion seems to involve connecting the corpse to a negative planar source which acts as a sort of pseudo-soul or driving force. That mindless energy source will naturally seek to consume life and create suffering as that will make it feel more fueled. I think it is the creation of the this negative energy engine and binding it to a body that is considered to be a fundamentally evil or evil-ish act. it isn't simply putting magical actuators on a skeleton from a unspecified power source, it is a very specific power source that even if mindless itself technically is naturally going to drive its animated object to want to harm and kill the living, just like plants naturally reach its leaves and branches towards the sun, and roots towards minerals and water. I feel it is personally, perfectly reasonable to say Good individuals can't bring themselves to preform that particular act normally, or at a minimum without some repercussion.
Could a neutral perhaps see it as a reasonable tool at time, if not abused? I can see it as a possibility. People have evil urges at time, and they don't always abandon them. However, if they actively curtail them and try to moderate them as they don't see them innately as positive, it is reasonable to consider they may not be falling into the Evil range, alignment wise. If you have a necromancer, raising undead, and using them to plow fields to feed the people who would otherwise die if they went int the fields they would be cut down by wild wolves eager to eat flesh? That might easily fall into a Neutral alignment. Not good, because the ends like that probably should not be seen as justifying the ends, but remaining net neutral might be viable. They might even 'idolize' good over neutrality or evil, but just like an addict might want to get away from their addiction, they might simply be unable to stay away, simply working to refrain, contain or control it as best they can.
While there could be something specific about body's that prevent them from being able to be animated with Animate Object, but I have to admit that an old enough corpse that the soul has already made it to its final resting place, I wouldn't really feel like rule-wise, I'd have a problem with it. And I would't consider it an evil act, since it wouldn't be powered by negative energy (and wouldn't have undead stats) instead it would be an animated object. That doesn't mean that people wouldn't still hunt you down and accuse you of disrespecting the dead, and/or accusing you of being a necromancer, because people are often not quite completely accurate in what they see.
The critical thing is according to the Rules, Animating Undead is an evil act. So any such spell doing an animation or creation of undead is invoking an evil and life consuming power. Animating an object using an Animate Object spell is not. If the local science lab skeleton from the local high-school fell through a dimensional rift and landed in the dungeon the adventurers are going through, it can be animated without invoking evil. This seems clearly defined.
Can you use Animate Object to animate a corpse? The SRD limits it to Non-magical objects. So technically, as long as the corpse isn't magical, and isn't being worn(ick), I think it could be legitimate target/object. This would not technically be evil, other than the potential of disrespect for the body. If it was done to allow a corpse to stand and move and return to its rightful resting spot after a earthquake for instance, I could see it as being perfectly respectful use of the ability, for instance.
If you want to create a Animate Vessel spell that binds a elemental (maybe even positive) or some other force to the body so that it becomes animated, that isn't a specifically evil. Feel free to do so. There are even fantasy examples where one might animate a recent dead with the soul of another already passed individual. If the host individual was a willing participant, or legally bound (by sentence, or such) then this might not necessarily have to be defined as an evil act, for instance.
Fundamentally however, I think Core Pathfinder, in Golarion; Raising/Animating Undead is inherently Evil and not a justifiable Good. Animating a Corpse, as an object (animate object), is probably quite frowned upon, but may not actually be an Evil act like doing so as an Undead. You want to play a good 'necromancer' maybe you can talk to your GM about allowing you to swap Animate Undead abilities for some kind of Animate Corpse ability. But if you look at the difference in spell level between animate undead and animate object. Animate Undead is obviously taking a shortcut. So an Animate Corpse ability would probably need to be weaker than the equivalent undead. It would probably need to lack the natural tendency to kill living things, potentially only moving and performing actions if specifically controlled, unable to make any decisions on it own. Perhaps it can't move to keep someone from passing through a doorway, or even attack creatures who attempt to bypass it, unless specifically directed to act at the moment. These limitations would make it less powerful, but potentially justify it no longer being directly evil.
So there are some options you could consider.
One thing to keep in mind is that doing evil acts such as animating undead does not automatically make everybody around you hostile. There could always be some cultural peculiarity or extreme circumstance that makes people welcome or at least be ambivalent about what you are doing.
After all -- How many people actually object to having Infernal Healing cast on them? If you keep your undead well under control and use them as an effective way to deal with the local community's enemies, the local attitude might be, "He's an evil guy, but he's OUR evil guy!"