Let's suppose that Elizabeth Shaw was right, that we had indeed been designed by extraterrestrial beings. Would that make them our gods, to whom we offer worship and homage? By the end of the movie "Prometheus" I think it is clear to Elizabeth that the answer is NO. She still believes that the aliens made us, but she now realizes that they mean us harm, and that we have the right to defend ourselves against them. Yet it's also clear that she has not lost her faith in God. It's reasonable to assume that Elizabeth has finally made a distinction between the proximal cause of our existence -- what was it that most closely in time was the cause of our coming into being -- and the ultimate cause.
ID proponents, such as I, could have strengthened Elizabeth's position that the aliens were our Engineers. We could point out that there is no plausible non-intelligent design explanation for the origin of life, and that it looks very much like someone designed the first cells. Most of us believe that God was the designer. But it seems to be at least logically possible that God was not the proximal cause of our existence, but that there was some intelligence that was the intermediate cause of our being.
There would still be the problem of what we commonly call our "souls." In the movie, it is pointed out that the robot, David, does not have a soul. We also find out that the aliens have indeed created a particular form of life that most of us would agree does not have a soul. For those of us who believe that that there are souls, would this be a problem for alien design? I think not. There seem to be two views of what souls are. Either they are a separate substance from matter, that has been put into an intimate relationship with it, that we call ourselves - soul and body. The second view is that there is some kind of emergent property in matter, such that if it takes the right form, it has what can be said to be a soul. If the first view is correct, then we can imagine that when the aliens design the physical parts that become us, at some point in time God infuses this physical part with the substance of soul. If the second view is correct, then once the aliens have put matter into the proper form, the property of being or having a soul will occur.
For those of us who believe in God, we could then, along with Elizabeth Shaw, still believe that we were designed by aliens. We might owe gratitude to them, just as we owe gratitude to our parents. But we owe our worship to the one God who is the ultimate cause of all of us, regardless of what planet we're from. So if on some starry night a flying saucer lands in your backyard and Kodos and Kang emerge and tell you that they created you and that you should worship them, just tell them you appreciate their bringing you into existence, but that there is only One to whom you will bow down.