First off, dandwiki has a bad reputation. I'm not sure who this is with, but I'd personally suggest using d20srd instead.

Here's their excerpt on Incorporeal Creatures (as a subtype):

Incorporeal Subtype

An incorporeal creature has no physical body. It can be harmed only by other incorporeal creatures, magic weapons or creatures that strike as magic weapons, and spells, spell-like abilities, or supernatural abilities. It is immune to all nonmagical attack forms. Even when hit by spells or magic weapons, it has a 50% chance to ignore any damage from a corporeal source (except for positive energy, negative energy, force effects such as magic missile, or attacks made with ghost touch weapons). Although it is not a magical attack, holy water can affect incorporeal undead, but a hit with holy water has a 50% chance of not affecting an incorporeal creature.

So let's quick break this down with a list of things that ignore incorporeality:

• Magic weapons
• Creatures that strike as magic weapons (including sufficiently leveled monks)
• Spells, spell-like abilities, or supernatural abilities.

Of these, there is a 50% chance to ignore corporeally sourced damage (such as fire), but will always take damage from positive energy, negative energy, force effects, or things that explicitly target incorporeal targets.

So the answer is: You can always hit with anything (as normal), but you may not harm the incorporeal target.

However, if you are doing the appropriate types of damage, you will always do damage, while other spells may not-this is entirely dependent on the spell in question. Cure light Wounds? You're set. Burning hands? Flip a coin.

Rules citations:

Animate Dead has the [evil] descriptor. "This is an evil act" is right there in the spell descriptor:

Evil: Spells that draw upon evil powers or conjure creatures from evil-aligned planes or with the evil subtype should have the evil descriptor.

Good Clerics can't cast [evil] spells:

A cleric can't cast spells of an alignment opposed to her own or her deity's (if she has one). Spells associated with particular alignments are indicated by the chaotic, evil, good, and lawful descriptors in their spell descriptions.

...But a Good wizard can.

The Alignment section calls out all [evil] spells as "minor acts of evil," and the creation of undead as a greater act of evil:

Characters using spells with the evil descriptor should consider themselves to be committing minor acts of evil, though using spells to create undead is an even more grievous act of evil that requires atonement.

Being raised as Undead clearly does something to your soul, because even True Resurrection, a spell that works even in the event of complete bodily destruction, fails if the target is currently undead:

This spell can also resurrect elementals or outsiders, but it can't resurrect constructs or undead creatures.

Note: The undead creature type contradicts this. The contradiction may be an error. It's also possible that it's intended for True Resurrection to work on undead, but that it doesn't return them to life as the undead creatures they once were.

So the rules are on your side, although perhaps not in a very satisfying way.

So far as whether or not it is moral for a Good character to create undead if that was what it took to do the greatest good... Well, that's a much more complicated question.

Just remember, in all alignment debates:

Alignment is a tool for developing your character's identity—it is not a straitjacket for restricting your character. Each alignment represents a broad range of personality types or personal philosophies, so two characters of the same alignment can still be quite different from each other. In addition, few people are completely consistent.

Why?

It's possible that the explanation you're looking for is out there. But to be honest, I doubt that it exists. You'll find plenty of definition statements along the lines of "creating undead is foul/evil/bad" (but why?). And you'll find plenty of examples of the creation of undead leading to terrible consequences (but what if we don't feed orphans to our undead minions?). But you're not likely to find a spelled out "creating undead does these bad things" paragraph.

The explanation of this is one of those things that takes a lot of talking to explain. It's a bit like the "airplane on a treadmill" problem, in that it has to do with very fundamental assumptions that people make.

The short version is that "what causes the creation of undead to be Evil?" doesn't have meaning in the Pathfinder universe.

Real Life

Here's how morality works in the real world. You have a fundamental force like electricity. I can use this force to do good (power a machine that cures cancer), or I can use that force to do evil (electrocute those who oppose me).

In either case, the electricity isn't good or evil. I'm good or evil because of the consequences of my actions.

The electricity could also come from a bad source. A power plant that runs on burning toxic waste, for example.

The person who uses the electricity will be judged on the sum of the consequences of their actions. If my machine does more good than the power plant does evil, and there are no better alternatives than the power plant, then I'm still a good person. I used a bad means to a good end.

In other words...

• A man does good, and therefore is good.

Or

• A man does evil, and therefore is evil.

Well, that's the simplified version. The philosophy of morality is extremely complex. But this covers a pretty good chunk of the popular definition.

Pathfinder

This game assumes good and evil are definitive things. Evidence for this outlook can be found in the indicated good or evil monster subtypes, spells that detect good and evil, and spells that have the good or evil descriptor.

In Pathfinder, Good and Evil are fundamental forces in the world, just the same as gravity and magnetism. You can detect them. You can measure them. Something can be fundamentally Good, or fundamentally Evil. This is not realistic.

In other words, Good is a thing, and Evil is a thing. Why Good is good and Evil is bad are left to the players and DM.

In other words...

• A Celestial is Good, therefore it does Good.

Or

• A Demon is Evil, therefore it does Evil.

A Celestial could do Evil, but it won't. Because it's Good. It can come into conflict with the protagonists, sure. It can be tricked, or fail in a way that results in a bad consequence. But it's fundamentally Good, and its actions flow from that.

The same applies to Demons:

Creatures with an evil subtype (generally outsiders) are creatures that are fundamentally evil: devils, daemons, and demons, for instance. Their redemption is rare, if it is even possible. They are evil to their very core, and commit evil acts perpetually and persistently.

This same reasoning applies to the Create Undead spell. The spell is fundamentally Evil. Using it causes an increase of Evil in the world, just as surely as a magnet is drawn to iron. There aren't rules for either of these things. They're the responsibility of the DM and the players to enforce through roleplaying.

Mortals

Mortals with an evil alignment, however, are different from these beings. In fact, having an evil alignment alone does not make one a super-villain or even require one to be thwarted or killed. The extent of a character's evil alignment might be a lesser evil, like selfishness, greed, or extreme vanity.

The section above applies to supernatural beings. Mortals get to behave more or less realistically... Their actions define their alignment.

You can take an Orc and raise it like a human, and it will be as likely to come out Good as anyone else. But if you do the same thing with a Demon, it will almost certainly come out Evil. Because Demons are Evil.

Spells

Spells are where things get messy. Mortals aren't bound to Good and Evil, but they can use spells, which are. This is the case with Animate Dead.

Animate Dead is Evil. The rules state this explicitly. There is no room for argument.

What that means, is left to interpretation. Perhaps it increases the amount of Evil in the wielder, gradually corrupting them and changing their alignment. Perhaps it increases the Evil in the world, making things inevitably worse.

It's unlikely that Pathfinder ever takes a stand on this issue.

Where do you go from here?

Fundamentally, you and your players have a different point of view. You're closer to the published materials, but that's slim comfort when you're outnumbered. Where you go from here is up to you... But you have a number of options.

Hardline Pathfinder

You could stick to your guns, and the Player's Handbook. Animate Dead is Evil. Period. Do some of the following:

• Show them this elegantly crafted essay.

• Make Evil be the result of the use of Animate Dead. All large-scale attempts to use it for Good fail.

  • Perhaps casting Animate Dead attracts Demons, or weakens a barrier keeping them away.

  • Perhaps it blights the land and corrupts the minds of those around it.

  • Perhaps it involves torturing and twisting the souls of those raised, denying them entrance to their afterlife for the duration (some support for this is in the rules, see True Resurrection above), and leaving them scarred for eternity.

• Like a magnet is drawn to iron.

Moral Relativism

You strike a compromise with your players. Animate Dead is Evil, sure. It's a perversion, and perhaps cruel, and definitely icky. But in the right hands, it can do enough good to counteract these cultural taboos.

• Play up the concrete consequences of the Undead.

• Limit corruption to the direct consequences of the spells used.

• At the end of the day, a great enough good justifies the use of Animate Dead.

Alignment Teams

Finally, you can disregard the moral implications of alignment altogether, and use it simply as a designation of teams.

• A "Good" alignment indicates that you act like Humans, Elves, Dwarves, and other PC-centric races expect you to act. You might be a terrible person, but at least you follow the rules.

• An "Evil" alignment indicates that you act like Orcs, Goblins, Drow, and other antagonist-centric races expect you to act. You've probably been unfairly maligned by the "Good" races. History is written by the victors, etc.

• In this interpretation an Evil spell is really just foreign. The Good aligned people would object to it, of course, but that's just their xenophobia talking.