The U.S. Army War College's Strategic Studies Institute has published a monograph called Islamic Rulings on Warfare (PDF), by Lieutenant Commander Youssef Aboul-Enein, a serving naval officer, and Professor Sherifa Zuhur, who is a visiting professor at the Army War College.
The monograph provides an overview of Islamic rules relating to war and refutes the interpretations of militant groups, showing that in fact Islam condemns the terrorism that these groups advocate. Check it out!
Added: This even got a little news coverage.