Hey Tycoon,
A number of the astronauts who went to the moon have professed various religious / theistic / spiritual beliefs, as have a number of the astronauts who have gone into space.
As much as your views as per "need to be religion-free" resonate with me, it's not overly likely to go that way, and I think there would indeed be some chance of sowing the seeds of discord with aliens just like we have done here on earth.
Remember however, that the chances of meeting aliens in which we are on a similar enough level to have a normalized exchange is very remote. The chances are much higher that the intelligent aliens will be much more advanced than us, at least if we were to meet in the near future.
Without going into all the argument as to why this is the case, witness the vastness of the universe and how quickly man has advanced in the last 5000 years and you should see my point about the unlikelyhood of meeting intelligent aliens on a level playing field.
A fair amount of the popular science fiction that is based on intelligent aliens posits at least a somewhat level playing field with the aliens, otherwise the story can lose it's human interest theme.
Check the "the overview effect":
http://www.bookrags.com/sciences/astronomy/religion-spsc-04.html
Wherever human beings travel, we bring our religions with us. "Godspeed, John Glenn," the farewell words spoken to the first American astronaut into orbit, exemplifies the characteristic human drive to carry faith into space.
Many astronauts who are religious have spoken of finding their faith strengthened by the experience of traveling in space. The ability to look back on Earth as a small blue planet, and to see the fragility of life and human existence, is an experience that brings many space travelers closer to the creator. The astronauts of the Apollo 8 mission, orbiting the Moon for the very first time in 1968, broadcast back to Earth a reading from the book of Genesis on Christmas day, in the belief that the passage discussing the creation of the world expressed their feelings of the awe and majesty of creation.
While some astronauts are agnostic or atheist, others have been highly religious. Astronauts from most of the major religions on Earth have been represented in space, including representatives of Islam, Christianity, Judaism, and Buddhism. Edwin "Buzz" Aldrin, one of the two astronauts who were the first men to land on the Moon, brought with him a small vial of consecrated wine and a tiny piece of communion wafer, in order to celebrate the holy sacrament on the surface of the Moon.
For other astronauts, the spiritual experience of space is not expressed in the terms of formal religion. After landing on the Moon with Apollo 14, Astronaut Edgar Mitchell founded the Institute of Noetic Sciences to reconcile the spiritual and humanistic values of religious traditions with scientific insights. The spiritual insight granted from spaceflight, and seeing Earth from orbit without political boundaries or petty human conflict, is profound. This insight has been tagged "the overview effect" by author Frank White.
