Have you read The Daughter of Time? Lots of interesting stuff about the spin of history in that, not to mention a pretty clear argument that Henry VII, not Richard III, ordered the deaths of those two little boys. I'm not an expert (my main focus of knowledge when it comes to English history is Henry VII's next couple of generations of descendants), but it makes sense to me.
The thing I always want to explain to conspiracy theorists is that I do believe in conspiracy as a tool of government. However, I don't believe in the kind they argue for. I don't believe in the kind of grand, overarching conspiracy that would take thousands of people to keep secret--if it's possible for it to have been kept secret at all. The example I want to use, however, is something they've never heard of. It's 350 years old and Scottish, you see. (I believe several important letters in the life of Mary Stuart, including the Casket Letters and the one admitting her place in the plot to kill Elizabeth, were forged, or at least had forged additions.) But if I am correct and that was a conspiracy, it was a conspiracy among a very small number of people indeed. It was to do one small thing which just happened to have large consequences. And once Mary Stuart was dead or deposed, depending on your plot, it didn't even matter to those people if their conspiracy was revealed, because it had accomplished what it needed to. And even then, people were speculating as the whole thing unfolded, so the only thing still a complete secret is who did it. And why should we necessarily know the person's name anyway?