Here's how I've been looking at the matter.
Firstly and most importantly, you have to remember that we're talking about good and evil as they exist in the game. This is not the same thing as morally right or wrong. Good and Evil in D&D are cosmic forces that predate the existence of sentient minds capable of pondering morals. Morality came later and was attached to these forces.
One of the key tenets of Good is the respect for life. Good recognizes creatures that show respect for life and put effort toward preserving it. This creates an undeniable, but not quite direct, link between Good and positive energy. If the enemy of my enemy is my ally, then certainly the enemy of my ally is also my enemy.
On the other hand, Evil recognizes creatures that kill without just cause, whether that lack is a result of the killing being motivated by something other than survival or the cessation of evil deeds or simply because the killing has no motivation.
Mindless undead will, if not controlled, seek out and destroy life. This is the result, I suspect, of positive and negative energies' tendency to attract and anihilate one another as is explosively demonstrated by the invariable occurence upon a xeg-yi and a xag-ya, energons composed solely of those energies given sentience (described in MotP), encountering one another.
Mindless undead are therefore evil, because their existence is defined by a drive to seek out and destroy life for no purpose whatsoever, barring the control of a sentient being. Useful tools though they may be, they are a mockery of life that will destroy life when given the chance. Creating such a being is evil because, in doing so, the creator has knowingly endangered the lives of everyone in the immediate proximity of the creature. He's also shown a callous disregard for the dignity of sentient beings, barring certain cultural setups.
The creation of intelligent undead is, in most cases, worse still. Most intelligent undead have the need to feed on the living. This leaves that unfortunate soul with the choices of being tortured by his hunger, causing suffering to still living creatures, or killing; not to sustain his unnatural life, but simply to ease the hunger or maintain some ability. The person who visited this hell upon another creature is either committing torture every second that undead creature is animate or spreading evil in the world by creating a creature that will invariably do evil for the sake of easing its own pain.
This is how I've made sense of it anyway. YMMV.