Anyone who wants to play the "necromancy is inherently immoral" card would also have to stop using soul gems.
Anyway, most of our necromancy spells involve raising ancient skeletons from the ground, rather than reanimating the recently dead. As such, the animus used to power these constructs is probably also very ancient and thus, not lucid.
Besides, Necromancy is mostly shunned because of Galerion's heavily biased bigotry and Mannimarco's deadly ambition. Couple that with the normal folk's fear of the unknown and there you go.
Also worth mentioning, our brand of Necromancy is mostly restorative and destructive magic. Sure, we use conjuration to pull some blank, unidentifiable souls out of the dreemsleeve (or maybe we take whatever is lingering in the local area?) but we do not deal with any Daedra. As you know, dealing with Daedra generally ends up with things going badly and often takes a powerful mage (aka the vestige) to control.
To sum up, Necromancy is only as bad as the person that wields it. After all, the Dunmer use it for ancestor worship, the Divine Prosecution use it to assist with solving murders, somebody has already mentioned Vastarie above, the Empire is generally ok with it as long as it is regulated, the Nords used it, the Khajiit mostly don't give a hoot (they actually do shallow burials for their deceased, well in the knowledge that it makes an easy target for a necromancer), the Bosmer aren't overly bothered either.
Some of those examples are feom different time periods and thus, are not relevant in 2E, but I still consider then valid.
So, just out of curiosity, do any of you Necro players give your character a reason as to why they would be doing quests and helping people? Historically, necromancers have always been pretty deplorable characters. Why would they decide to help others?