The Seraphs go after Flonne for "killing" a human, except the human is in my party, alive, well, at full HP, with new equipment and a couple pupils too to boot. (Okay, the pupils are a work in progress.)
I tried replaying the level without having Flonne ever enter the field, but I got the same cutscene. Did I screw up at some point?
You didn't screw up. This is a scripted part of the story. Merely harming a human is a "grave sin" and I suppose it doesn't matter if she actually struck the blow or was merely a co-conspirator in the crime. This is actually an important plot point in the story. Ultimately Flonne will be punished for her sins. How exactly is one of the major differences between Disgaea's endings. What you did on the Primordial Soup map doesn't have any more effect on the ending than what you do on any other map.
