The world factbook was mostly things that the military or politicians might care about the truth of, and data they need anyway. Mostly what is there were things where there wouldn't be much value in spreading lies - and what value that might have is outweighed by you can fact check everything (with a lot of work) so lies are likely to be caught.
Not saying they are perfect, but this isn't a place where I would expect they would see distorting facts help them.
It's definitely not the worst that can happen. Happens fairly often - google: CIA lying to congress. Getting audited is the worst that thing that happens to the CIA. ie The U.S. Government Accountability Office (GAO) last actively audited the Central Intelligence Agency (CIA) in the early 1960s, specifically discontinuing such work around 1962.