The ends justify the means. - attributed (perhaps unjustly) to Niccolo Machiavelli

Christian proponents of Just War Theory would surely reject the quote above as being entirely antithetical to their doctrine, but are no doubt committed to 'doing something'* in response to the spread of evil. With these things in mind, how do they formulate an appropriate response to a foe that does not share their inhibitions in terms of means used? For example in asymmetrical warfare, insurgents who utilize terror tactics will often be aware of the principles that their enemy operates under and will exploit them for maximum effect - utilizing human shields, booby-trapping corpses, or using children to carry explosives etc. - what are the relevant principles that ensure that a Just War can continue to be prosecuted both justly and effectively in the face of tactics such as these and not sacrifice one at the expense of the other? Which, if any, scripture references are used to support these principles?

*This is a reference to the quote of Edmund Burke in the counterpart question to this one:

The only thing necessary for the triumph of evil is for good men to do nothing.