They could do a great detail to keep this from being a war on Islam, by being more cooperative with anti-terror efforts, and by working to eradicate terrorism from the Islamic community. The fact that they see it as a war on Islam indicates that they are taking at least some cues from radical preachers, which does not bode well. From the [1] Washington Times, with thanks to Ali Dashti:

More than one-third of American Muslims believe that the U.S. war on terrorism is really a war on Islam, according to survey information released yesterday by researchers at Georgetown University.

Thirty-eight percent of American Muslims polled said they believe the U.S.-led invasions of Afghanistan and Iraq, and the tensions with Iran and Syria, reflect a foreign policy that is targeting Islamic countries and Muslims themselves.