It would be a little inconsistant (and again, very X-Files) to bring in a government conspiracy at this point in the story. Hopefully all these flashbacks are building to a larger picture that makes sense in the Lost universe.

Whether or not there is a cover up of their being survivors or not, I wonder if they are going to move the story to a point where we find out flight 815 was set up to crash. And also if we ever find out why. I just hope the pregnancy thing isn't the end of the story, interesting as it is.