"Three may keep a secret, if two of them are dead."
Conspiracy is hard. If you don't have actual legal force backing you up, it's nearly impossible to keep information from spreading out of control -- and even legal force is by no means a sure thing. The existence of the Groom Lake air station, for example, was suspected for decades before publicly available satellite images made it pointless to keep up even the pretense of secrecy.
For an extragovernmental example, consider mystery religions. These aren't too uncommon: they're not as popular as they once were, but new or unusual religions still often try to elide the deepest teachings of their faiths, either for cultural/spiritual reasons (e.g. Gardnerian Wicca) or because they sound as crazy as six generations of wolverines raised on horse tranquilizers and back issues of Weird Tales (e.g. Scientology).
Now, where's it gotten them? Well, Gardnerian Wiccans will still tell you they're drinking from a vast and unplumbed well of secret truths, but it's trivially easy to find dozens of different Books of Shadows (some from less restrictive breakaway lineages, some from people who just broke their oaths) that agree on the broad strokes and many of the details of the Gardnerian mysteries. (Also many others that bear almost no resemblance beyond the name and some version of the Lesser Banishing Ritual of the Pentagram, but never mind that.) As to Scientology, Operation Clambake (xenu.net) had blown that wide open years before South Park popularized the basic outline of what's charmingly known as "space opera"; these days it takes about ten minutes to fire up a browser and pull down a more-or-less complete set of doctrinal PDFs by way of your favorite nautical euphemism. Less if it's well seeded.
"But these are just weird minority religions," you say? "Knowing this stuff doesn't actually harm my spiritual well-being, because I only care about the fivefold kisses when my SO's involved and there's no such thing as body thetans"? Sure, but the whole point of a mystery religion is selecting for conviction. Typically they're gated by an initiation period measured in years and thousands of dollars, not to mention some truly hair-raising oaths; I don't find it plausible that science broadly defined can do much better.
You are clearly right that conspiracy is hard. And yet, it is not impossible. Plenty of major events are caused by conspiracies, from the assassination of Julius Caesar to the recent coup in Thailand. In addition, to truly prevent a conspiracy, it is often necessary to do more than merely reveal it; if the conspirators have plausible deniability, then revealing (but not thwarting) the conspiracy can actually strengthen the plotters hands, as they can now co-ordinate more easily with outside supporters.
Successful conspiracies, like any other social organization, need incentive compatibility. Yes, it's easy to find out the secrets of the Scientology cult. Not so easy to find out the secret recipe for Coca Cola, though.
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