Some useful bibliographical pointers to places where Foucault discusses the question of war from Philippe Theophanidis, beginning from this 1981 quotation.

Therefore, if you like, I never stop getting into the issue of law and rights without taking it as a particular object. And if God grant me life, after madness, illness, crime, sexuality, the last thing I would like to study would be the problem of war and the institution of war in what one could call the military dimension of society. There again, I would have to cross into the problem of law, the rights of people and international law, etc… as well as the question of military justice: what makes a Nation entitled to ask someone to die for it.

As Philippe notes, Foucault’s discussion of (civil) war is not just in ‘Society must be Defended’, but also in the newly published La Société punitive. The indications are that there will be further discussion in Théories et institutions pénales, which has extensive treatment of popular revolts. See the full post at Aphelis for all the references.