Before I give you another suggestion I want to make clear I am not trying dissuade you from making the story at all. I am merely trying to help you make it in a way that makes sense and flows well. Believe me, all I am trying to do is help.
Well I prefer to stick with the plot as well, even in a SW&LotR crossover I still made sure it would not contradict anything in SW's main plot so I chose to start from the end of current TOR story, which they haven't given the new plot out yet, and avoid original characters unless no existing character could fit the role.
Well, since she could take the risk to work with a Sith Lord who killed countless Jedi and betrayed her ancestor before, permit her Jedi to aid her ancestor with the genocide plan and that frame thing, I think she would consider this. It's not she couldn't kill Malgus later.
Now, before you go any further with this play through the Jedi night story. You will get a better idea of things. Now think about this (warning, spoiler here if you have not already heard, which i think everyone in their grandmother has by now) who would be better suited to potentially have a child powerful enough to possibly destroy the Empire> Satele and Malgus or a Jedi who killed the Emperor? Malgus I wouldn't consider being the Sith father as he, at this point in time, is most likely unable to father a child.
You can still have the capture of Shan, but that could be the lure to get your Knight to come to herr rescue and succumb to the plan. Just throwing this out there for you.