The only reference to god or religion that I noticed was the doctors necklace. And its role was only a couple minutes long. I think someone had something on their brain before they saw the movie.
Did you go to the bathroom during every conversation with the doctor and the one wearing the cross? The whole purpose of them going there was to find their creator despite the fact the main characters all wanted to believe in god except the blonde captain. I knew there was trouble when the female scientist was in cryosleep talking to her father about death and all the religious nature of that pointless scene. Did you miss the 7 or 8 references to christ in that whole scene, or were you in the bathroom again? Then the female doctor always wanting to believe in jesus no matter how much they were showing jesus had no presence on earth. There was the whole basis of intelligent design which was the whole purpose of the opening scene and the idea that these being supposedly put the human race where they were. Oh, and then there is the best suck you out of the movie and into pointless life drama when her boyfriend makes the crack about only needing a couple of brain cells to make life, and then she goes into her pointless crying jag implying she was barren which did not add anything at all to the movie and was the first time reproduction was even mentioned. In all honesty considering what happened that scene might have actually been valuable towards enhancing her character had they actually done something more on development of that aspect of her character.
There is a lot of religious bullshit in this movie, and Alien is not religious. If they wanted to do some sort of Contact type of philisophical commentary on god and science it was not the right movie. That might have been a good movie on it's own, but it is not alien, and I am quite sure the company does not give a fuck about God or even the alien races that supposedly spawned humans. They wanted a weapon from an advanced civilization. They actually may have tried to make a statement about the lust for power that keeps the human race down, but they kept on dropping it to go back to blind faith.