Is it of value to state explicitly in my book that the Secret Space Program’s purpose was not to create an earth defense, but a mercenary force under extraterrestrial control to use against humanity?

This is the time and this is the place. Why tell half a story if the whole story can be told? This will bring into focus at once the reason for compelling levels of secrecy to the extent of manipulating the individuals involved to erase their memory in many cases and to confound and corrupt their minds in ways that persist following their service. The oath of secrecy and loyalty has served quite well in the military and intelligence agencies down through history with very, very, few exceptions, and would be sufficient in this case if the Secret Space Program were simply a human/extraterrestrial cooperation needing to be done in secret for preservation of cultural stability, for example, or other reasons to keep the potential advanced technology in perceived safer hands and not have it fall to governments that are untrustworthy or likely to use them unwisely, at least as perceived. The dark doings need to be hidden, and the darkest of the agenda is the ultimate goal they have in mind for creating this partnership—which is human destruction.