Because the just war tradition developed with conventional warfare in mind, it is legitimate to ask how (and if) it should be applied to the fight against terrorism, a fight that is often fought using unconventional or irregular means. I believe that the answer is that it should because the goal of a just peace is one worth fighting for but only if it is fought for justly. In particular, the principle of non-combatant immunity should loom large in how the problem of terrorism is tackled. How we can apply this principle to the fight against terrorism can be illustrated when considering the practice of targeted killing, a practice that the Israelis made famous (Walzer, Thinking Politically, p. 274). An obvious objection to the practice is that it is no different from assassination and thus prohibited by the just war tradition. That, however, is not true. The just war tradition only prohibits the killing of political leaders on the assumption that at war's end, a peace agreement will need to be hammered out with such leaders. It does not rule out the killing military personnel or enemy combatants, which the terrorists clearly are (Walzer, Thinking Politically, pp. 274-275). Thus, on the face of it, it appears that the practice is permitted by the tradition since, by definition, the practice of targeted killing seeks to avoid the killing of non-combatants.
That said, it cannot be stressed enough that the authorities need to take extra care in making their targeting decisions (Walzer, Thinking Politically, p. 275). This, however, can be quite difficult since terrorists often seek to blend in with the crowd, making detection more difficult and the loss of innocent life more likely, which is why we have to be as sure as we can that we can hit targeted persons without killing innocent people who are nearby:
Here I think we have to adopt standards that are closer to Philadelphia than Afghanistan. In a war zone, collateral damage cannot be avoided; it can only be minimized. The hard question in war is what degree of risk we are willing to accept for our own soldiers in order to reduce the risks we impose on enemy civilians. Bur when the police are chasing criminals in a zone of peace, we rightly give them no latitude for collateral damage. In the strongest sense, they must intend not to injure civilians--even if that makes their operation more difficult... That seems to me roughly the the right rule for people planning targeted killings... They can't avoid imposing some degree of risk on innocent people, and the risks will certainly be greater than those imposed by police in a city at peace, but we must insist on a strenuous effort to minimize the risks” (Walzer, Thinking Politically, p. 276).Targeted killing is not the only option, however, and it may not be the most desirable one. Research has shown that terrorist networks are remarkably resilient and often are able to recover quite quickly after a key leader has been eliminated. Moreover, terrorist groups generally suffer more "damage" if one of their members is captured or (better yet) defects. Defection, in particular, can shut a terrorist group's operations down for weeks or months because the group doesn’t know what information has been passed to the authorities (Eli Berman, Radical, Religious and Violent). Of course, getting someone to defect is easier said than done, but reconciliation and amnesty programs in Indonesia and Singapore have met with some success. Other evidence suggests that policies aimed at eliminating the structural conditions that help give rise to terrorist groups in the first place (e.g., building alternative schools, improving economic conditions, eliminating ungoverned spaces) can all be effective in reducing the prevalence of terrorism as well.
Most likely no single strategy, by itself, will do the trick. Instead, we will need a combination of them. Moreover, these alternative (and non-lethal) strategies, however, require an acknowledgement on our part that the fight against terrorism is ultimately a long one, which given our tendency to be an impatient people, makes adhering to the principles of the just war tradition all that more difficult. Nevertheless, if a just peace is our goal, if we want to help create a world where individuals are free to flourish, then I don't see where we have much of a choice.