User blog comment:FairyRaven/Fairy Tail Chapter 416: Tartarus Arc: Final Part, Review and Commentary/@comment-112.198.90.159-20150119172538/@comment-9595671-20150119181016

I think its because Zeref only wanted to kill Hades, it was basically how he punished him for attracting Acnologia. Rustyrose and Kain only did what Hades asked them to do, so he chose to spare them.