There's a simple fix to this problem. It's fine to consolidate the standards into one set of guidelines to apply to all crime programs but some minimal level of suspicion in the form of factual justification should be required before the FBI or any other federal law enforcement agency can open an investigation, targeting a group or an individual.
To gauge the seriousness of the problem, the Justice Department's IG should immediately undertake a review of all "terrorism enterprise investigations" begun by the FBI after 2006, which was the end point of the IG's prior investigation that found problems.
--The blurring of protest activities and dissent with terrorism dovetailed with the launching of U.S. wars after 9/11. For example in October 2003, the FBI put out "Intelligence Bulletin 89" focusing on plans for the upcoming protest of the Free Trade Area of the Americas meetings in Miami and anti-war marches in Washington, D.C.
I personally made a complaint to the Justice Department's IG about this blurring, but it was sent back to the FBI and then swept under the rug. Other complaints were treated with similar disinterest or disdain.
When New York Times reporter Eric Lichtblau exposed the bulletin, the Justice Department retaliated by yanking Lichtblau's press pass (and the FBI ordered its 56 field divisions to cease contact with the Times reporter. The sorry episode is described beginning on page 122 of Lichtblau's book, Bush's Law: The Remaking of American Justice.)
Perhaps if the government hadn't adopted that overly-defensive posture, the problem would not have reached the proportion later found in the September 2010 Report: "A Review of the FBI's Investigations of Certain Domestic Advocacy Groups."
The wrongheaded mindset that dominated law enforcement almost immediately after the launching of the Iraq War (and larger "war on terror") is most clearly seen in what a spokesman for the California Anti-Terrorism Information Center (CATIC) said when forced in 2003 to defend his agency's unjustified targeting of anti-war protesters without any factual evidence.
CATIC Spokesman Van Winkle, apparently without thinking too hard, reasoned that evidence wasn't needed to issue warnings on war protesters.
"You can make an easy kind of a link that, if you have a protest group protesting a war where the cause that's being fought against is international terrorism, you might have terrorism at that (protest)," said Van Winkle, "You can almost argue that a protest against (the 'war on terror') is a terrorist act."
In a similar vein, the Department of Defense (DOD) was caught after years of administering its annual mandatory anti-terrorism test that equated protest with terrorism. The correct answer on the DOD test for "What is an example of low level terrorism activity?" was "protest."
Also noteworthy is the fact that Joint Terrorism Task Forces (JTTF) and Fusion Centers combine the local and state police jurisdiction with federal jurisdiction. So crowd control -- something properly handled by state and local police but not usually within federal jurisdiction -- becomes something the JTTF can "jointly" do.
It's even possible that CIA membership on these joint task forces and fusion centers gives the spy agency a role although the CIA is supposedly barred from operating domestically.
The fix here would be to stop equating protest, including acts of civil disobedience, with terrorism.
The Patriot Act's definition of domestic terrorism begins with these words, "Acts dangerous to human life," meaning that exercise of rights to protest and dissent, even acts of civil disobedience involving minor crimes like trespass and/or entailing some property damage, do not constitute acts of terrorism.
Issues of crowd control, even during large marches and rallies, do not normally implicate national security and are not normally matters that federal authorities should be involved with.
--A front-end loading system of "statistical achievements" is the main way of evaluating job performance inside the FBI and probably in the other 3,000 some agencies and contractors believed to now be operating in "Top Secret America."