Define militant islam as a terrorist movement; give it the same stigma and legal status that communism had during the cold war.
Require muslims (or the whole population, heck) to certify they do not belong to any religion that advocates the violent overthrow or conquest of another country, and that they specifically foreswear and abandon parts of their "religion" that call for those things.
Give the law some teeth.
And require would-be immigrants or visitors to the U.S. sign a declaration that they are not, never have been, etc., associated with a religious organization that advocates violent overthrow or conquest of other countries or religions.