Here's the kernel of what seems to have happened, synthesizing both the Crane reporting from the Guardian today and the Drake indictment:
1. Drake favored a competing dragnet surveillance system that was pushed aside in favor of Trailblazer.
2. Drake lodged a complaint with the NSA IG that Trailblazer was a waste of money with inadequate technical controls. He is joined in his complaint by William Binney and several other former NSA employees.
3. Concurrently, Drake began leaking to reporters --- presumably, James Risen and Eric Lichtblau, who broke the first major NSA surveillance story for the NYT --- using Hushmail.
4. In handling Drake's formal complaint, the NSA managed to leak Drake's identity to DOJ. The article is fuzzy about exactly which law this violates (it refers to the Whistleblower Protection Act, much of which does not apply to national defense and classified information, and not the ICWPA, which has different procedures and protections). Either way: the White House is apoplectic about the Risen/Lichtblau scoop and uses the leak to raid Drake.
5. In the course of investigating Drake, DOJ discovers (perhaps by first ruling out Binney and the other original complainants) Drake's Hushmail leak. Drake is prosecuted.
The Guardian article would have you believe that Drake was prosecuted directly for blowing the whistle through formal channels. But that is not at all what seems to have happened. Yes, in the process of investigating Drake's complaint, there was a procedural foul (Drake's name shouldn't have ended up at DOJ). But it wasn't Drake's formal complaint that got Drake in real trouble!
Again: I think Drake has the most sympathetic case of all the NSA whistleblowers. His leak was extraordinarily targeted, not particularly political, and clearly in the public interest. I'm not writing to litigate whether Drake was right. I'm saying: the Guardian did a poor job of reporting this story.