He was indicted and more. He plea bargained and he was convicted.
It's not "BS" about protecting secrets- that's the same reason Agee was never nailed as much as he deserved, the SOB pulled the old trick of calling every covert agent and anyone remotely related to covert ops as witnesses. Rather than expose agents and methods it was regrettable better to nail him with only the base evidence and not try for the big stuff that would open the proverbial can of worms, maybe get people killed, American and allied assets.
These weenies, evil unethical lawyers and really dumb emotional juries - the latter having "reasonable doubts" no matter how much evidence of guilt is presented - are the reason "secret evidence" rules were sought. Prosecutors know the odds of getting an inteligent jury are about nil so they won't take the chance and prosecute more difficult charges with greater penalties. But if we just had smart juries with a capacity for logic many prosecutors wouldn't have to open doors better left shut - they'd be able to work with the information available.
That said, there is no doubt the DOJ is corrupted- there are elements who become tenured over the years who will protect mafia-connected people ... and certainly the Clinton cronies are mafia connected as we know from Hillary and Harold Ickes. In the Berger case it is more likely his connections saved him, otherwise prosecutors would have made absolutely certain he was ineligible for any kind ofsecurity clearance. That they didn't extract this from him is proof the prosecutors were sympathetic to him or at minimum paid off.
Yipes. Now if I could just get in the habit checking my spelling so I could catch my skippy keyboard before hitting "post" I wouldn't look like a candidate for the next grand jury...
these aren't "secrets" worth protecting, they are secrets worth revealing - the extent to which the government knew of AQ operations inside the US before 9/11, as presented in the millenium after action report - who wanted to do something about it, and who did not.