But this makes me wonder again, what the hell did the Kurtas do?

The Kurta didn’t necessarily have to do anything. Nobunaga himself said they were once like the Hei-Ly, driven by anger and resignation to lash out at the world, implying they’re not quite in the same place they were before. It could be that the message they left behind after the massacre was just something they always did for their jobs early on, lashing out at the world and letting everyone know it was them doing it. The Kurta were a part of the world outside Meteor City, so were subject to their wrath. I think the point is that the Troupe were dehumanized and victimized by the world, and so went on to victimize and dehumanize the Kurta, treating them as just another treasure to steal, not that the Kurta were somehow guilty and deserving of death from the Troupe’s perspective.