Originally Posted by
Psyren
It's true that negative energy itself isn't evil - but neither is radioactive waste, and pouring it into a lake or meadow would still be an evil act.
Per Libris Mortis, negative energy makes it easier for uncontrolled undead to enter the world that the necromancer didn't intend. There are a vast quantity of undead creatures that can arise spontaneously from various circumstances, and LM/BoVD state that unchecked necromancy can mean more of them. Nobody knows exactly what makes some executed serial killers become Mohrgs while the others simply die off for example, but in nations where necromancy is widespread, you will get more of the former. Similarly, not all neglected children become Slaymates and not everyone who dies with unfinished business becomes a Ghost, but the ones that do likely do so due to some presence of "ambient" negative energy.