Here's one idea i'm considering using to address the issues:
You need a vessel and a spirit to animate something.
A body is a vessel;
the spirits used to animate undead come from the lower planes, lemures or their equivalents. Thus justifies all undead and their creation being evil. This is done because it's cheap. The lower planes provide these spirits at low low prices (25 gp/hit die for some!). While the spirits may be lemures, the providers are higher-ups in the evil system, who have the authority to rent out these souls.

You can also animate using elemental spirits (like golems), or wholly artificial spirits (some other constructs). It's possible to animate a body using the same processes as construct animation, it's just a LOT more expensive (several hundred gp per hit die); as such most people use the evil option.
Other aligned spirits (good, neutral, etc) can be used, but it tends to be a lot harder/expensive; and a lot more selective about who they're willing to work/provide spirits for.