That was it. I had possessed her multiple times, but it kept telling me that I was missing something. I mistook the walkthrough with Leanne saying if you slept with her you don't get the romance path and figured that meant as Mother Superior as well.There is no bug in this process, I am pretty sure.
To not get kicked out, did you possess Mother Superior TWICE. Did you have sex with Thrall Leanne as Mother Superior.
After sleeping with her as Mother Superior it worked fine (I never spoke with Sarah Gates though for that ritual).