We have to assume so cause she created the bloodline spell and also I think later confirmed she was trying to rid the world of all vamps.

She knew, as she says that before returning from the dead she convinced the spirits to let her fix their biggest mistake, which was to make them immortal and only she knew how to kill them, in addition to the fact that this is evident when Ayana says that later they would become "the beginning of a plague" which they actually became, they just failed to present the beginning of the lineage with the Trinity vampires, Klaus should have killed Esther when they went to France together, and not before, after all they already they had become vampires and it would make much more sense for her to know that the white oak stake actually killed them, that part of the story didn't make any sense.