The point is that you cannot equate a religion with what some of its adherents do, have done, or want to do. All large religions even Buddhism has had violent madmen committing crimes in their name.
Its vices and virtues untold, Christianity has left its violent phase behind, and so has the mainstay of Islam. By equating the vast majority of Muslims with the archaic and aggressive groups, you make it hard for people to distinguish, and you make it much harder for moderate Muslims to distance themselves from the terrorists, because you are really asking them to swear off their religion.
So the basic answer to your basic question is: We cannot wage war against Islam, because Islam is not the problem. Certain Muslims are the problem.
Hans