I still don't know why Charlize Theron's character was in the film. Yeah, I get the relationship she has with her pops mirrors that the human race has with the Engineers, but that whole story line really doesn't need to be in the film. ... If you take out Charlize's character, it doesn't change the story one bit. The only thing she really does is not let the infected Dr. Holloway back on the ship when he's infected, and that action could have easily been given to another character--anybody still on the ship.
I really enjoyed Prometheus, and am a huge fan of the Alien series in general. I have now seen Prometheus twice but not the extended version, and have read a few articles about it but not a lot. So some of this may be contradicted by other sources, and it's all tainted with my enjoyment. But here's my explanation for the raison detre of Vickers:
As a character, the most important role that Vickers played was to be rejected by Weyland. To understand this, you need to back up a bit and review one of the key themes of Prometheus: the creation of life that comes from the sacrifice (i.e. destruction) of the creator. This self-sacrifice is a key philosophy of the Space Jockeys. It is shown first hand in the opening scene where a Jockey kills himself to start life on a desolate planet, and is the basis for their biotech. Rejection of this philosophy and embracing entirely selfish principles is (ambiguously) the reason they want to destroy mankind.
If Weyland had no offspring of his own (for either biological or sociological reasons) creating David as an artificial son could actually be a sympathy provoking act, as some sort of last desperate attempt at reproduction. Likewise, it's critical for us to see that Vickers has made a (begrudging) attempt to shepherd her father across the galaxy and help him fulfill his goals; if she had been left on earth it could be because she aggressively rejected him instead of the other way around. But by shunning his own flesh-and-blood offspring that is willing to serve him in favor of David, Weyland becomes a true monster. This is the reason that the Jockey kills Weyland (with David's body) when he is awakened; as emissaries for mankind, an old man who refuses to die and his artificial son are the embodiment of the abomination that the human race has become. If Weyland had met the Jockey with Vickers present, the confrontation would have been entirely different.
Vickers' character also exists to embody a number of key symbolic roles and relationships, more than the one possible allegory you mentioned. Vickers' backstory is designed to be the exact opposite of Shaw's; Shaw was motivated by the death (sacrifice) of her father, while Vickers was motivated by her father's refusal to die. And Vickers and David combined are the recreation of Weyland; they are opposite sides to the same coin. They are obviously juxtaposed in a number of ways (male vs female, emotional vs apathetic, etc), but they are also similar in their goals, stubbornness, and acting.
Plotwise, Vickers plays a number of seemingly minor but critical roles. For one, she is the one who distracts Janek so that Millburn and Fifield are not heard when they are attacked. The fact that she does this with sex is interesting as a comparison to David (who uses sex as a weapon to infect Shaw), to Shaw (who has sex for love while Vickers has sex for pleasure), and to the original Alien movie (which is partially an allegory for rape). I suppose the role of distractor could have been acted out by someone or something else, but it wouldn't have had any of the sexual undertones.
In an even more important role, Vickers is the only reason that Janek ejects the escape pod before ramming the Jockey ship. She is the only person left on the ship with selfish motivations that is more concerned about saving herself than saving humanity. This is obviously critical to the end of the movie, and the role could not have been carried out by anyone else without creating another self-driven character specifically to fill this role.
So I think Vickers is pretty critical to the movie. I also give credit to Theron for her acting job in it, simply because I recognize how hard of a role it was to play. So much of Vickers' mannerisms and motivations are controlled by others, and so much of Vickers story is told in scenes where she isn't present that it must have been really difficult to understand and portray the character properly.
