Ahm, her dynamics with Bajaj is damn weird. Kinda relates to Stockholm syndrome. That's an extreme case of someone who's held hostage developing feelings for the person who's responsible for that. Here too, she's stuck with Bajaj - you could call it hostage coz she doesn't have an escape, yeah walk out of the deal whatever and all.
Her family has disowned her and her lover is practically a goner. Anurag is going gaga saying he'll take back Prerna etc, but unless she reveals the truth and stop his impending "moving on in life" track, even if he succeeds in taking her back with him from Switzerland, their relationship has turned toxic as per status quo. Anurag isn't happy coz his love is gone, Prerna isn't happy coz her lover is going mad, to such an extent that she is accompanying Bajaj to deal with her sense of grief. That is the extent of toxicity in their relationship as she has chosen to hide her "sacrifice". So even if he takes her back (not possible), they aren't gonna be like happy or anything until she tells him the truth. So their happily ever after in the foreseeable future is a goddamn myth.
So, lover gone, family gone. Someone like her who's independent to the extent of standing on two feet alone with not a penny to her credit (Haven't ever seen her work or anything, I doubt she made some money), has right now, no choice but to take refuge with Bajaj. So that's why she's following him despite hating him.
As to why she's a puppet, well, coz now I have started seeing the signs of a quintessential, stereotypical husband-wife appearance between Bajaj and Prerna. Especially in the train when they give each other looks after Anurag came and sat there. So, she hates her husband but he's her husband nevertheless. Hence the sad portrayal of a puppet. Would it have been different if she had been with Anurag? Ahm, not really. She'd have been burdened with "mature" and Mary Sue responsibilities. My tap is leaking, Prerna would fix it, someone's in the hospital, Prerna would operate on them, someone's in jail, Prerna would get him or her out. That' could be a sense of independence but it would be over burdening cares reducing her to a donkey carrying more than required load. 😆
Such a long post, in one line, Prerna's character is deemed to be doomed in the future. That's how it's been written. So can't help.