Family relations and parenthood is probably the one big underlying theme in the film. The characters go out in a search for our "parents", and find they have issues with them although they don't understand why. You'll find that most of the main characters address at some point the notion of being somebody's son/daughter or parent.
Shaw has dreams in which we see her father. He is the one who told her to believe whatever she chooses to believe in, and apparently raised her with an open mind (especially towards other people's beliefs and the possibility that religion does not give us the true answers, but that it's not a problem to believe anyway).
Vickers was thrown in there because she embodies the issue of bad parenthood. Weyland has more love for his android (his creation, his "son") than his daughter, because he is so in love with himself (does he not program the mission because he wants to become immortal?) he cannot love a being that was born out of his love for another person (Vicker's mother). Instead, he is prouder of his "son" who was designed and built by him and his company, and shares more traits with him than anyone else could. If Vickers wasn't there as his daughter, he'd just be a grumpy old man who never had any child and finally decided to build one, and that would be touching. Instead, her being his daughter turns him into a self-centered SOB, and shows you the issues that arise when you make becoming a parent about yourself more than about the child.
The issues in parenthood between David and Weyland are obvious (kill the father blah blah blah). Shaw cannot become a mother, and then gives birth to a monstrous creature... Hell, even that sociopath Fifield refers to his little probe droids as his children, and establishes himself as the leader of a wolf pack, with the little drones being the wolves pups. And then of course there are the Engineers, our "fathers" (By the way do they have females? Scott is big on motherhood, the mother characters in his films are always strong, or trigger strong emotional reactions from his male characters ex. Leon in Blade Runner "I'll tell you about my mother"... Is Scott trying to depict the flaws that would be inherent to a society that's entirely controlled by "fathers", who can seed life and end it as they please whenever it becomes a threat to them, with no mothers to save them?)
The theme of parenthood is everywhere in this movie.
If you want to say that the Weyland / Vickers "twist" was poorly executed, or gives the impression it was thrown into the mix without being really thought-out to allow us to care about it, then I agree. But if you say that it is not necessary, I think you're wrong : it's another element that says something about the movie's main theme, and something important if you ask me.