Driving Islam underground is not a solution. What it needs is sunlight and exposure. The war is coming--let people see the enemy.
Photosynthetic weeds grow in sunlight, but not all harmful organisms are photosynthetic.
The danger is not that people are allowed to practice Islam, but rather that the religion is then used to harbor other things. Further, I think more publicity about Muhammed himself would probably be a good thing. Let everyone know what sort of person Moslems consider to be beyond criticism, and what sorts of behavior they are thereby endorsing.
Christians recognize quite a few great people in their religious history, including David and Solomon. Only one, however, is considered to be beyond criticism. Obviously no mere human can aspire to truly be like Jesus (since he was divine while humans are not) but people can seek to follow his example. As for the rest, they are recognized as being imperfect, and people are advised to avoid their imperfections.
From what I can tell, Islam teaches that Muhammed is beyond criticism; everything he did was good. Thus, Islam fundamentally contradicts any moral code that would condemn the types of things Muhammed did. While there's no problem with someone who accepts Christianity and yet condemns the actions of some of the people who spread it, it's fundamentally impossible for someone to accept Islam and yet condemn its first prophet.