He was an evil mass-murderer. Does it matter how it went down? Absolutely.
It matters to one of the fundamental humanitarian principles of the laws of armed conflict: if they are "hors de combat," or "outside the fight," then targeting even military objectives is a war crime.
So first, was bin Laden a military objective? Assuming one accepts the idea that the United States is at war with al Qaeda, yes. In war, persons who directly participate in hostilities or who perform a continuous combat function in an armed group are targetable, and bin Laden certainly was the latter, if not the former.
But what about "hors de combat?" Here's what Protocol I to the Geneva Conventions says:
A person is 'hors de combat' if:
(a) he is in the power of an adverse Party;
(b) he clearly expresses an intention to surrender; or
(c) he has been rendered unconscious or is otherwise incapacitated by wounds or sickness, and therefore is incapable of defending himself;
provided that in any of these cases he abstains from any hostile act and does not attempt to escape.
The first reports had it that bin Laden was armed and put up resistance by using a woman as a human shield. Subsequent reports said wrong, not armed, no human shield.
Does that render him "hors de combat?" No. It does not amount to either (a) or (b) or (c), above.
Some law of war theorists claim that a person who poses no evident threat is also "hors de combat" (To keep my students interested, I call it the naked soldier hypothetical). But unless and until that idea finds its way into the Geneva Conventions or into the practice of a substantial portion of the world's militaries acting out of a sense of legal obligation, it will not be the law.
What about the fact that he was an evil terrorist with the blood of thousands on his hands? If he was "hors de combat" that would be a matter for judge and jury to sort out, not Navy Seals. And that's exactly as it should be because killing in war is not for the purpose of implementing justice. It's for the purpose of neutralizing the enemy. I won't argue with President Obama's conclusion that "justice was done," but I do think that term is more appropriate for what comes from a (legitimate) court of law than the end of a gun.
But what if you reject the "war against al Qaeda" paradigm? In that event, human rights law, rather than the laws of war, would be your guide. And human rights law prohibits arbitrary deprivation of the right to life. While the legality of lethal force is a closer question outside of armed conflict than in it, the totality of circumstances make it difficult to claim that the killing was arbitrary, even if bin Laden was not actively resisting or fleeing.
All in all, probably a legal kill assuming the official version is true.