(1) A “kill order” would be illegal if there was a practical alternative, such as capturing OBL. (I don’t mean “pragmatic” in the sense of do we want to try him etc., but “practical” in the sense of what the troops could reasonably do on the spot.)And I agree with a VC commenter that, if international law or the laws of war hold that what we did was illegal, then that indicates a problem with the law.
(2) If OBL clearly surrendered when troops encountered him — hands in the air, say — and his capture was a practical alternative, then the troops had a duty to offer quarter.
(3) Troops have no duty to negotiate a surrender with someone who doesn’t immediately offer one, particularly in circumstances like this raid into Pakistan.
(4) Whether OBL was a civilian or not is not terribly important here. He’s a terrorist, hostis humani generis or however one spells that, and not entitled to avail himself of a soldier’s means when convenient, then hop back onto the civilian side when convenient. He was owed minimum protections under CA3, but no more.
The best objection is that we trespassed on Pakistani sovereignty, but that still isn't a strong objection. Either (1) Pakistan was harboring OBL, or (2) Pakistan is so dysfunctional that rogue army/ISI elements could harbor OBL, and warn him of any raid. In the former case, that's practically undeclared war on the U.S. In the latter, Pakistan is not a state whose rights we are bound to respect; it's a glorified Afghanistan, a failed state whose corpse hasn't begun to stink yet. Where normal legal processes don't obtain, other powers have the right to use military force. Obviously, had OBL been hiding in a London flat without the UK's knowledge, we wouldn't have sent in the SEALs -- we would've told the Brits and let them pick him up. That wasn't an option here.
Finally, Yglesias has a good point: if OBL really wanted to give the U.S. a problem, he should've walked into the U.S. embassy in Islamabad and turned himself in. Yow.