What is relevant is whether a body of thought or set of doctrines espoused by some organization can exist within a broad legal framework founded upon rational definitions of individual rights such as free speech, freedom of the press, property rights, due process, etc. Whether or not a certain ideology takes issue with applications of these principles is not important. However, if an ideology by its nature opposes the very foundation of this framework AND actively seeks to undermine this system through violent means, i.e., the initiation of physical force, such an ideology moves from the status of "religion" or "ideology" to an active enemy of
Shinto is an ancient Japanese religion and did not present a threat to the United States until it received state sponsorship and became part of a nationalist movement which sought global domination and attacked the United States in 1941. Communism actually began as a religious movement in the centuries before Marx secularized it in the 19th century. Even then, it was still not a "threat" until it too received state sponsorship and it's followers made their goal military conquest and global domination. Once an ideology receives state or some form of organized sponsorship and actively seeks to overthrow western governments, it becomes a criminal enterprise. Any offshoot, whether it is actually sympathetic or not to the more radical leadership, is then fair game to be investigated by our government and sympathizers arrested or deported.
Certainly, during World War II, any organization sympathetic to the goals of the Japanese Empire or the Nazi's would have rightly been shut down or arrested by the U.S. government and treated as enemy combatants depending on the extent of their activities. Communism was merely a kooky philosophy until the Bolshevik revolution of 1917 followed by other movements which swept Europe and Asia, i.e., it was not a threat until it found state sponsorship and attained the goal of global domination, threatened our interests, or engaged in either outright or proxy wars with the United States. At that point, communist organizations which espoused this ideology ceased to be protected under the First Amendment, and became an objective threat to the existence of our government.
Many have said that the fact that there is not an obvious state sponsor of Islam and the fact that it seems to have many degrees of radicalism makes it more difficult to identify whom we are to fight.
First, once the proper principles are identified, the task becomes much easier. One needs to ascertain the state sponsors in terms of organization, finances, and training starting with the most radical first. Once these sponsors are crushed, the various offshoots become marginal, just as some random sympathetic Communist, Nazi, or Shinto organizations were neutered once the Soviet Union, Nazi Germany, and the Japanese Empire fell. Until the time at which state sponsorship and a global threat is neutralized, anyone identifying themselves with Islam must be regarded with suspicion and there should be an objective legal framework for investigating any ties to more violent organizations as we did with Communists in the 1950's or the Japanese and Nazi's during World War II or British loyalists during the American Revolution. I would make the same argument against Catholics if the Vatican declared its goal to be world domination under the rule of the Pope and Vatican law and were to actively fund and train an army in this effort.
Second, I think the primary state sponsors of totalitarian Islam are obvious. Iran is the heart and soul of this movement followed by Saudi Arabia and Syria. Rather than focus on rogue tribes hiding in the mountains of Afghanistan, we should be confronting the elephant in the room - Iran and its countless financial and military allies which fund, train, and support radical Islamic groups throughout the world. While this occurs, Islamic organizations in the United States should not be treated as a protected "religion," but as sympathizers to America's enemies and since they identify with our legal and objective enemy, the burden of proof must be on them to show that they are not sympathetic or do not in any way directly aid and abet these global sponsors.
Third, because the freedom to speak and practice religion are sacred pillars of the American system, it is vital to objectively define and delimit the government's function as it relates to defense, i.e., define precisely when it is necessary for the state to use force in the protection and furtherance of individual rights. I have no illusion that the current American regime has any ability to fulfill this obligation, and I understand those who are concerned that such powers could be used as a precedent to persecute any political opponent of the state arbitrarily deemed to be "dangerous." I suggest the above as a blueprint precisely because the situation calls for a strictly objective formulation in order to delimit this use of force.