Same issue here. You get the XP for finishing the quest, but not the faction reputation. I tried reloading, leaving Roseway, restarting the game, but the issue persists. Not sure what would happen if you also sold the research to Gladys.
I convinced Cassandra to hand over the research, sent her to the Iconoclasts and got the guards to leave peacefully. 8/12 rapts were killed but the matriarch survived. Playing on PC.