“Raise Dead creates an Evil creature, and creating an Evil creature is an Evil act, per the rules. Period, end of story.”

I understood that as analogous to real-world pollution. The undead are animated by the hunger to consume all life, where the hunger to consume all life is a physical thing. You could put it in a jar. And you could leak it into the rest of the world... Sure, just one skeleton won't pollute the world very much, but it will pollute even if you only order it to do good things.