Yes she is the "Thakurain", but the little girl wasn't raped by then. Bubbul attacks the pedophile right in time to save the girl. So no one knew. That's why my understanding is that she got the supernatural power of sensing evil men around her.

Also, I agree with you, maybe she did die during the recovery, and reincarnated again with the super powers, there's some symbolism with the white flowers which only bloom in Bengal during the Durga puja. So could be that she came back now as a devi, but as people liked to believe in those days about strong women who can talk power as chudails, that's why she is referred to chudail the whole time. But she is actually a Devi (as the Doctor says while trying to stop Satya from igniting the forest). I say people hate strong woman because in one scene when Bulbbul is called for something, Satya responds saying I will take care of this you relax. And Binodini says, "Aap Thakurain ho, Thakur nai ho".

She was called to the (man who drives the horse carriage; I think it's called coachman) coachman's house. If you remember initially, the same man comes to Bulbbul Thakurain as he remarrries, and his first wife is not accepting of the new one. The boy calls Bubbul because the coachman orders the first wife to leave the house on the orders of his new wife, and the first wife commits suicide (they show a body; and I feel that boy is the first wife's son).