It's hard to say whether it should be surprising that Operation Northwoods was committed to paper on government letterhead. An official government document proposing terrorism against the American people. And throughout history there were 53 admitted false flags: http://www.washingtonsblog.com/2015/02/x-admitted-false-flag-attacks.html .

So it becomes fair to wonder what was so big about anthrax, and why Matt deHart had to be arrested on trumped up charges.

On Page 88 of Part 10 of 59 on the FBI's released Amerithrax investigation, a psychological profile without letterhead is provided. There are also presumably letters from Ivins against fat people near the beginning of the PDF file.

But if the CIA was responsible, would the FBI know, or would they have been just doing their jobs? It's a pretty power argument for people just doing their jobs when virtually every Nazi gave it as a reason. You'd have the BAU giving facially a specific profile, but in reality about 1% or so would qualify, so it'd fall under Schneier's arguments for no terrorist catching system is effective (although clearly it won't be completely automated). Then you'd have field agents under pressure to solve the case, they might just be rationalizing why what their doing is correct.

For all it takes for Bruce Ivins to be falsely accused is for the CIA to stay mum, and for the FBI to do their jobs?

In proportion to the punishment, murder convictions are inaccurate, one in nine are exonerated based on retested DNA evidence. The CSI effect is quite fortunate, or that rate would be higher, the police only gather enough evidence to ensure a conviction, not to ensure they don't have an innocent person. The probability that OJ was guilty was in all fairness, 40%. Another 40% it was Jason. 20% it could've been anyone else. Legally, no prosecution for murder should succeed by official standards.