Whe For a short period, prior to ratification of the Bill of Rights, the Constitution included a Declaration of War but not any Freedom of Religion. And the First Amendment rights have long been recognized to not be absolute. You can't cry 'fire' in a crowded theater. Because you might panic those within into a stampede and get people killed trying to get out. Pearl Harbor could as well have been considered as an attack from Shintoism under leadership from its living God, Hirohito as it was considered an attack by a Japanese 'nation.' The two were congruent. Their Kamikazes were done with elaborate religious rituals. But that didn't stop us from declaring war. And that didn't stop the Shinto religion from being modified by us in their defeat.
Whether Islam should even be considered a 'religion' is debated. It certainly is more in scope than conventional religions at the time of the Framing. Arguably its very un-American political and legal features are more important than its 'religious' ones, yet it claims to be an indivisible hole. Jefferson didn't understand it when he met Muslims in Paris during that Revolution while the Constitution was being written over here. He obtained a Koran to try to learn more about it. We value our Freedom of Religion, at least those of us on the right. Making limitations for any self-professed religion would be a difficult step. But if La Raza wants to resume wielding obsidian blades in sacred Aztec rituals in my country I expect to invoke sacred American rituals, like the Second Amendment. If modern 'Aztecs' claimed they couldn't have their religion without human sacrifice, well then no such religion allowed. If Muslims become sufficiently obnoxious and aren't willing to divide the obnoxious practices from their indivisible Islamic whole, well then no Islam allowed. If that ends up requiring a Constitutional amendment, one would pass when needed.
If we are to eventually end up at war with all of Islam, a daunting prospect, it still may strategically make sense to start out piecemeal and delay the final reckoning to more favorable circumstances. Which may call for creative definitions of the enemy. History records many series of small conflicts leading to definitive ones. And responses less than 'war' may be in our interest at times. But to let our enemies hide behind the First Amendment until we're dead would be making the Constitution into a suicide pact. It's not.
I understand perfectly what you're saying, but in order to avoid any Constitutional conflicts, war could be declared on a country (or countries) and ALL their people could be ejected from the US.
Gitmo is a perfect example. Had we declared war, those men would have been enemy combatants, and could have been treated as such. Instead, they were treated as civilians in temporary custody with all their human rights intact.
I'm not saying islam isn't a problem, and I'm not saying ISIS and other such groups shouldn't be dealt with, but creating more problems by going about it wrong is not the answer.
Just my 2 cents.