Little Green Men exist in Star Trek. Therefore, the bible was proven a novel (Which, I think it is) the day the Vulcans landed on earth (2064??). It makes sense that Star Trek doesn't recognize God. (At least the way the Bible says we should recognize him).
Sorry...You can't have it both ways. Either you believe in the bible or you believe NOTHING like Star Trek will EVER be true. (Thus, a lot of my problem with organized religions).
Just my thoughts...
At the same time, I don't spend my time poring over the bible looking for references to automobiles or nuclear war, I take it as it is and let it inspire me with prayer and reflection.
At a minimum for my faith not to be shaken by contact with intelligent alien cultures, I would have to see *some* evidence of the same God that I worship in their own culture.
I am not an expert on this subject, but when Western missionaries first started visiting China and studying Chinese, they were excited by what they believed were references to the Christian God embedded within the Chinese calligraphy system itself. These ideas are still taught today among Chinese-speaking Christians. I would at a minimum look for some reference to a concept of sin and a need for an intermediary for remission of sins.
I think the Ferengi could be a big problem, unless Christians just decide they are the spawn of Satan...