The problem here seems rooted in a few paradoxes in the rules.
The spells for creating and/or animating dead are all of the [Evil] descriptor. This means, by letter of the rules, the spell detects as evil with a detect evil spell (and palading ability). It can be interpreted that casting such a spell is also an evil act, but at best it is a neutral act.
Rebuking undead is the purview of neutral or evil clerics and is an ability provided only by neutral and evil deities. It requires the channeling of negative energy. The servant of a good deity would certainly see the reliance upon morally flexible (neutral) divinities as pushing the boundaries of goodness, if not plain unethical.
The planar traits of the Negative Energy Plane and Positive Energy Plane clearly indicate that neither is aligned in any way. Neither one has an alignment trait. Both are antithetical to life as a character knows it, though positive energy is life edifying in smaller amounts, while negative energy is life denying in similar amounts. Anti-life certainly equals evil in many minds, but this is a philosophical point. However, evidenced by the attitudes of most undead, connection to the Negative Energy Plane seems to make the creature in question seek to destroy life, because...
Almost all undead are "always evil." The exceptions are ghosts (any alignment) and mummies (usually evil). Since most undead are always evil, manipulating them even to a good purpose could, philosophically, be seen as trucking with evil. In a morally absolute sense (see below), it is probably neutral behavior at best. The paladin is right to think this sort of behavior is unethical, if not evil--regardless of who the "stiffs" once were.
Alignment, in core D&D, is a moral absolute, thusly allowing spells to affect targets based upon their alignments. FR, by the letter of the rules again, relies on the same sort of moral absolutes. It could be argued , therefore, that trucking with evil spells (creating undead) is morally evil in an absolute sense. Whether or not the spellcaster is evil, the act of casting such a spell is evil. By this token, the paladin is also correct in her assumption that the necromancer is not a worthy companion.
Also, skimming the dogma of Tyr in Faiths and Pantheons, the Tyrrans seem to be little concerned with undead in a general sense, unless those undead are lawbreakers or harmful to the weak (likely). A Tyrran is also interested in enforcing local law. Is the use creation and manipulation of undead legal in the territory in which the game occurs? Is it legal within any canon of law with which the paladin is familiar? If not, there’s trouble a brewin’.
The Fist of Raziel class requires the character to be a warrior against evil. Righteousness probably demands she not associate with persons who use evil magic. In fact, it may demand even worse repercussions.
Just about everything else, including many things posted here, is a philosophical issue, not a rules example.
BUT...
Is this the type of game you're running? What you've suggested with your post is a less-rigid system of moral definition. If you've fudged this system to make a more flexible morality, does the paladin's player understand this?
Is the necromancer's culture evil? Within the rules of the core D&D game, it seems unlikely for it to be anything better than neutral. It accepts the casting of evil spells (according to the rules again) as a cultural norm.
(Diverging from the topic.) We see in Eberron examples of moral flexibility. Unfortunately, this doesn't help much, because the Eberron milieu (and, indeed, core D&D through Book of Exalted Deeds) creates a whole new monster type for "good" undead tied to the Positive Energy Plane -- the deathless type.
Would that hey had just altered the undead type to accommodate undead tied to positive energy, but this makes it harder to write rules. It's easier to just write "undead" or "deathless" than it is to write "undead tied to negative energy." That the "Any alignment" ghost is still an anomaly notwithstanding. Perhaps, since you’re using Book of Exalted Deeds, you should house rule a few things, such as good undead (including baelnorns and archliches) all being actually deathless, evil undead remaining the same, and neutral undead an unknowable middle ground (some are deathless, some are undead.)
(Back on topic.) If your campaign allows for moral flexibility (unlike core D&D) wherein the manipulation of (evil) undead can be good based on the motivations of the manipulator, you should explain this to the paladin’s player. Then he or she can make an educated decision based on the truth of your campaign world. There’s no arguing with that.
(However, "what if" scenarios exist to thwart even this line of reasoning. The paladin could argue that the act of creating evil undead is too risky, even if the motivation is good. What if the party were killed before they destroyed these corpse minions? Harm would eventually come to others for this careless and selfish act.)
This, then, really becomes a problem of a lack of definition of the game world in terms of how morally flexible the alignments are. You need to correct that. If negative energy creates undead and positive energy the deathless, then the "necromancer" should really be converted to a character with power over the deathless. (Unfortunately, only Eberron has spells that allow the creation of deathless, though such things should be easy enough to extrapolate from create undead and others. Yes, regarding what s/LASH asked, these spells use positive energy to animate corpses.)
Whether or not the DM enters the debate, the DM has to know how the cosmology of his world functions. A character, such as a paladin, needn't have faith or mere opinion on the matter of whether animating the dead is good or evil. She can use detect evil and the answer is right in front of her eyes.
Still, the characters’ coming to grips with a moral quandary is great for roleplaying purposes. (This supposes you, as DM, understand the true moral nature of the use of undead within your own game.) Will they be able to reconcile their obvious cultural differences?
Anyhoo, my 2 coppers.
