When I say that war crimes are an inevitable byproduct of war, am I trying to excuse the Bush Administration?
No. The point is that when you choose war, you choose war crimes--and that this is true regardless of why you are choosing the war. You may be going to war for reasons that even the staunchest of libertarians would support, like defending your territory from violent attack. Just the same, if the war grinds on for any length of time, you will get people violating the Geneva Conventions, doing obscene things to enemy soldiers (dead and alive), and launching attacks that would horrify the population if they were watching a third party do them. By the time you're a year or so into it, the public and the soldiers are reacting to the last attack and the mountain of dead, not to who started it. Dresden would have been unthinkable in 1939; by the time it happened, anything was justifiable if it saved Allied soldiers.
There are better and worse institutional safeguards against this sort of thing, and the most charitable thing you could possibly say about the Bush administration is that they seemed wholly indifferent to the need to maintain those safeguards. But this, too, has nothing to do with whether we were the aggressor; it's a matter of military culture and administrative decisionmaking.
Naturally, occupations breed certain sorts of transgressions, because the population is resistent. But occupation is hardly the sole province of the aggressor. It's certainly far from clear to me that our current occupation is producing more such incidents, or breakdowns in the justice system, than our occupation of Germany did.
The civil war is producing lots of war crimes committed by Iraqis and foreign terrorists on other Iraqis. But though I agree that we have responsibility for stupidly unleashing a civil war, you can't really categorize a suicide bomb in a market place as an American war crime.
Likewise, I am against the media management. But it's rather milder than what we've done in wars that were indisputably just.
The point is, these things are part of the cost of war, not of the cost of "wars started by the Bush administration" or "wars with bad motives" or "wars we don't like". Sometimes, they are a cost that is worth bearing. Often, they are not, and if I were to consider whether to support a future war, I would weigh them heavily. But they should be weighed even if you think the war is just and right, because they will happen.