Inside Rebellion: The Politics of Insurgent Violence (Cambridge Studies in Comparative Politics) by Jeremy M. Weinstein
Scratch this one - a limited study that seeks to prove a somewhat monocausal thesis - that insurgent brutality is dependent on the sources of insurgent funding. It has all the weaknesses of any monocausal explanation and is written in academese to boot.

I would suggest adding Resistance and Control in Pakistan by Akhbar S. Ahmed and Uncomfortable Wars Revisited by Council member John T. Fishel & Max Manwaring. Also Stathis Kalyvas has a bunch of his research papers up on the internet, which make excellent free reading here.