Well, I was in Alwan's faction. My mistake was that, instead of sabotaging Teygen's pathogen, I accidentally *helped* them make it. So, I went back to an old save and killed the agent and everyone else inside the spire, thus stopping the process. I suppose that was considered very rebellious but I couldn't find another way to sabotage it.
It worked, though. Alwan was pleased and I was able to get to the cutscene where loyalist assassins attacked me.
Thanks for all your input!
EDIT:
Hmmm....it seems that was *too* rebellious. When I entered the Shapers hall I got thrown in a cell, Game Over.
I guess I better go back and find a less destructive way to sabotage that agent.