"Who gets to decide which US citizen does and does not get Constitutional protection?"
You're presuming that the majority of al Qaeda supporters and sympathizers are US citizens. I don't believe that to be true. Even if it were, do you actually believe that Thomas Jefferson intended to allow the "Mohametan" to slaughter the "Infidel of every denomination," utilizing his own writings to protect themselves while doing so?
Try to step back from the religious angle long enough to see that the terrorism is what is wrong. That it is primarily associated with Islam is something of a red herring. Many former Nazis, who fled and went into hiding to avoid prosecution, were at least nominally Lutheran. Would you have proposed that we (or any Israeli agents in the US) were Constitutionally prevented from pursuing them?