If we go back to Cold War days, what would your position have been regarding the legality of the Communist Party USA. The party was illegal in the US in some sense was it not? I believe that Islam is much like the Communist Party. American Islamic leaders have openly declared that IF they can become a majority in this country they intend to replace the US Constitution with Sharia. The Communist Party would have also done away with the Constitution if they had been able to obtain majority status. I can't think of a single other world religion in the US that has as its objective the supplanting of the Constitution. Everywhere in the world where Islam is in contact with another of the major world religions we see conflict and bloodshed.
One of the risks of democracy is that people will use democratic means to take power and then put an end to democracy - that's true whether the anti-democratic philosophy is religious, political or economic. A democratic nation must trust that the power of democratic ideas can preserve freedom.
What is the alternative? Banning the practice of Islam and prohibiting the posession of Islamic articles in the United States? Redefining the GWOT as the Global War on Islam? If so, then what is the end state of our campaign? What does success look like?
Seriously, what end state can we realistically achieve with the instruments of national power available to us if we make Islam the enemy? We also have to consider the 2d and 3d order effects of our actions.
There are an aweful lot of Muslims in the world. We have to deal with them somehow. Do we 1) destroy them, 2) dominate them on their home turf, 3) build a wall between us and them; 4) influence their culture in ways that are advantageous to everyone; 5) submit.
Those seem to be the only options to me. Right now, our primary strategic goal is #4 (influence), but we're also doing a little of #1 (destroy) where needed and #3 (defend) as well. But these are secondary strategies. I would argue that we are not doing #5 (submit) at all, but that we are doing "respect" as a part of our overall #4 (influence) strategy.