I don't see how contact with an alien race would be any sort of faith problem, personally.
Well, for me, that would be entirely contingent upon whether they seemed to possess the same set of intrinsic moral code that is contained within the human race or not. If my belief is that
A) God Created everything
B) God created humans(and in this case, other lifeforms) in order to have a relationship with them.
C) God's moral code's are His own and don't vary by race
Then it follows that any species would share a certain number of essential moral codes....don't murder, don't steal, etc, etc. If the alien species had no concept of a "God" and their sense of justice or "morality" was completely foreign, then I would argue that would yield serious implications that Theists would need to reconcile with their faith.
Not having a concept of God could be a simple matter of not having been exposed to the concept by others--i.e. humanity and any other races that do have such a concept.
As for the sense of justice and morality...you may notice that even the higher mammals often seem to exhibit traits that look like precursors of our own sense of those things. Not only are they right from the moral perspective--but justice and altruism do in fact further the species biologically as well as physically. So I think you would find major cultural differences--but I'm not sure you'd find that total absence of anything to relate to that you suggest. It wouldn't even be a good thing from an evolutionary standpoint, let alone a spiritual one.
About your comments on a mass extinction event--depending on how one interprets Revelation, there may even be a promise of some sort of cataclysmic event inherent in it. Guesses as to what and when are futile, and there is even Scriptural basis to say that attempting to guess is spiritually destructive. (And I can say, based on behavior I've seen from those who DO try to guess, or get too absorbed in it, that this is true.) So personally I do not see any promise for there not to be a mass extinction event. Added to that is the fact that there is also the promise of a new creation. That cataclysm would not be the end as it would've been had humankind all been destroyed without Jesus' sacrifice ever occurring (which is another thing to note about Genesis).
Now I am not a theologian or a scholar--those are just my thoughts.
