I doubt that Seren did this stuff deliberately to stop Zaros or anything like that. She states in her broken form before TLW that she went wrong somewhere along the way when she showed the Mahjarrat the rituals, and that they became violent. It's possible that she intended them to return to Mah so she might be cured, but she didn't predict that they would end up fighting each other to pick a sacrifice.
As for the Zarosian faction, she mentioned in the memoriam device that she would have helped Zaros with the ilujanka problem if she wasn't occupied with the elves. She also said that the Empire secured peace in the world and ensured that Tirannwn would be untouched; this is also apparent when Zaros ordered Char and co to check on the Serenists and report back, without being detected. This suggests that Zaros was worried about her as a sibling. And when it comes to her relationship with him:
Player: "But I thought you and Zaros didn't get along?"
Seren:
"I distrust, despise and sometimes even hate my brother Zaros. But I also love him. Whatever comes between us, whatever trials we face, he is still the only brother I will ever have. So forgive me if I dislike someone trying to take him from me."
Player: Are you happy she's returned?
Zaros:
"Yes. Does that surprise you? Whatever we are, however many times we squabble, we are still the closest to family either of us will ever possess. Seeing her whole again means there is hope that we may yet reconcile."
These statements suggest that although Seren said that she would stop him from transcending, she isn't going to kill him. And also that Zaros wants to patch things up with her and make sure she's safe, as he confirmed to Serenist players in FOTG.