If you want to go with theories about governments hiding something (or a bit more than that), you could argue that the whole reports of alien life out there are more a smoke screen than anything else. For example, I, the President of Somewhere, could let one of my trusted advisors mention a secret site dedicated to some kind of research. While most of the attention is focused on this secret base, nobody would question my hidden activies at producing unconventional weaponry; in this case, Master of Orion III: Deluxe Edition.
My point is, I would be hiding secrets by letting something much less important "slip". Note, however, that this is not necessarily my opinion in this matter, but merely a random idea (on this particular matter, I would be very surprised if anyone had a good knowledge of alien life, provided there is alien life advanced enough to pop in and say heya).
About religion and aliens: another conception could be that there isn't just a single one deity, but quite a few of them, with each one (or more than one for this matter) at the head of a particular people (and possibly closer to Ancient Greece pantheon). It would be difficult to explain why aliens have never been mentioned in the past however; but similar changes have happened in the past (such as a change of mindset towards the human body, among others).
Deadstar, your First Contact Protocol seems to be lacking an entry: what happens if they nuke us, rather than the other way around? In this case, is the solution 1 applied (Nuke'em right back, that will teach these pesky aliens), or solution 3 (sue for peace, and backstab them as soon as possible)?
*Goes back to looking for huge yellow ships in the sky; we won't be caught unprepared this time! But where did I put my towel...*