I don't know if we can outlaw the entire religion because it would present serious constititional issues. Who knows, there may even be some benign forms that would compromise the attampt. However, any members of any organization that advocates the violent overthrow of the government can be charged with sedition. I can't explain why Ashcroft has not dusted off this option.
Sedition was proscribed in 1798, but Jefferson refused to enforce it. It was then revived in 1917, but overturned in 1921. One last time, it was tried with the Smith act of 1940, which is no longer in use.
The reason is that being a free country, you're free to want to overthrow the government. If you should choose to advocate violent methods to that end, we have laws against inciting riots, violence, conspiracy et al. In short, the United States makes a clear distinction between the idea, and the action.
There's a problem, though. If orthodox Islam is as much a political force as it is a religious one, the suppression of ALL Islam becomes necessary on the grounds that as long as any Islam exists, there is a grave danger of a fundamentalist reformation which will then declare jihad on us all.
The First Amendment states that "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the government for a redress of grievances" (emphasis added). What's more, this has never been interpreted to allow treason nor lies.