I have an interesting way to play this:

The necromancer uses the undead to help people rebuild. They are essentially free labor that he uses to perform great acts such as building a new town hall, plowing fields for a town stricken with illness, or any other number of heroic or charitable acts. Maybe the towns he helps can even build mausoleums in his honor where people can volunteer to have their bodies stored upon death, so that should he need more bodies to perform his charitable works, the towns can provide a steady supply of donor-bodies.

He wouldn't have to make it some 'moral grey area' where he steals bodies to perform good acts. He's a folk hero, right? Maybe he has enough of a reputation as a 'good person' for people to willingly donate their own bodies, or the bodies of their loved ones, for the greater good. (Kind of like organ donors, or people who donate bodies for science.)

That way, there is nothing 'evil' or 'ambiguous' about his necromancy.

It could also be a good point of tension with certain NPC's and PC's when they refuse to donate their bodies, or some religious zealots view his necromancy as a bastardization of morality despite people's choice to donate their bodies.