You don't need to cast Animate Dead to function as a necromancer, so that would be simple enough.
Yeah, except that Animate Dead is pretty much the quintessential Necromancy spell, the single most potent visual symbol of that branch of magic. Besides, Gordon is Levels 8 (Fighter) -> 2 (Mage) when you can first meet him (he lives just off Waukeen's Promenade), and it makes a lot of sense for Gordon to have self-motivated his studies by refusing to wear armor or use his sword until he has learned how to raise the dead. Of course, I could easily change that to Death Spell, another milestone in the necromantic reportoire, but that would put him at Levels 11->2, which is far more EXP than the party could have by that point.
As for the precise ethics of casting Animate Dead, it's worth saying that BG and D&D are
two separate games (whether or not they
should be is a thorny topic indeed), and that none of the spellcasters in the game, not even Aerie, show any compunction about the spell at all. I believe Valygar does in one of his banters, but then again I may have my signals crossed: I know I wrote an anti-Necromancy banter between Valygar and Gordon, but I'm not sure there's already one with an existing NPC.
BG2 is 2nd edition with touches of 3rd, and some mod content is even bringing in 3.5. In the interests of leaving NPCs like Gordon more possible, I'd like to keep Animate Dead as 'Gray' Necromancy, perfectly acceptable for Neutral characters to use.
Side note: What exactly does Turn Undead do to those Undead who are destroyed by its effects? Suppose Anomen calls up a few Skeleton Warriors to help him out, and when the battle is over he Turns them, so that they don't have to serve him any longer than necessary. Does this cause their souls any harm? Would dispatching them by hand be more humane?