Inter enim arma, silent leges
current mood: unimpressed
... is roughly translated as, "In the face of arms, the law is silent" (Wiki suggests it is more properly rendered as Cicero did: "silent enim leges inter arma"; YMMV, but I do not wish to digress). It is a legal maxim that expresses the tendency of civil legal protections to give way to military necessity, as the internment of Americans of Japanese descent during World War II (which was ultimately repudiated, but after the war was over). It was rejected outright in the Civil War, despite the exception to Habeas Corpus in cases of rebellion or invasion explicitly provided for in the US Constitution (apparently b/c Lincoln didn't seek Congressional approval),and more recently in the Guantanamo detainee case Hamdi v. Rumsfeld.
And, ya know, I don't have a problem with that. However, I must say that Cicero's argument appears to have more applicability in dismissing the charge of "Crimes against Humanity" one Daniel Fiol has laid against Barry O in the International Criminal Court at the Hague. Much as I might like to indulge in schadenfreude about Barry O the War Criminal, the charge is bullshit.
In a CQC assault on a terrorist safehouse, you don't have time to say "you're under arrest". If a known hostile does anything except instantly put a pair of empty hands up in the air, he's bought 'n' paid for - you can't give him time to reach for a suicide switch. This is the essence of "inter armes, silent leges" - civil law cannot apply in the middle of battle, because there's no time for reflection.
Even granting arguendo that this guy might have a leg to stand on with his argument (and, he may not even have legal standing before the ICC to file), among other guarantees and limitations, the Peace of Westphalia, as I understand it, made (and still makes) waging war the exclusive province of nation-states, not individuals or non-governmental organizations. Any individual who tried to throw down on a foreign power was declared outlaw, and pretty much had no rights or protections. See also Piracy and the traditional summary execution of pirates. We have since extended limited protections for outlaws who submit to capture, but there we are again - military necessity in the assault made it practically impossible to take him alive without his full and complete cooperation. Guess bin Ladin should have thought about that one before he decided to wage war on his own hook. (Historians, feel free to revise and extend on this)
As far as the argument for Pakistan's sovereignty being violated, tough cookies - the Hague Conventions require a neutral sovereign to prevent belligerents from using its territory, and allows the other belligerent to pursue into its territory if the neutral doesn't or can't comply. Here, Pakistan was a putative ally - so, tough cookies, twice over.