"I am not quite libertarian enough to think that there is no place for secret investigations in our legal system."
I am. For what the FAuthor means, that is: against anyone. The government can go ahead and secretly investigate all the non-citizens it wants, but U.S. citizens are^Wshould be a protected class (under the Constitution). [And the only protected class in this country, BTW.] It should be *extremely* difficult for the govt. to get a citizen on a crime. That should be considered a good thing. Instead of perverting our system and making it easier for the government to go after its own citizenry, the non-corrupt way is to do both of:
1) Granting citizenship (including and especially de facto!) judiciously and limited in numbers, and
2) Incarcerating longer.
If mass govt. surveillance and other abuses were removed, along with the attitude that everyone is a potential criminal, and they had to instead operate as if everyone is innocent, and will always be, until it was evident that someone wasn't, there'd be some healthy resistance to expanding our ranks, and if they had to prosecute someone, it would take so much work, they'd want to make it really count.
"Is the FBI investigating a terrorist cell that is likely to steal softly and silently away into the night if they are notified that their banker is onto them?"
Too bad. If the terrorists are U.S. citizens, arrest them on suspicion, and if a judge denies them bail for being a flight risk, then so be it, if not, tough titties. Flipping through the channels on Fri I think it was some host on FNC asked "what do we do about lone wolf terrorists". The answer is nothing. Not everything has something that can be done about it. That oftentimes won't make the overall situation worse. We need to rekindle our pride in ours being a "shit happens" country. For what that means in a broader sense.