I think we're using the instrument of 'war' for an end which it is not suited for. As you point out, we're not engaged in total war, at least not any more. The lines are clearer in that case: kill or capture all soldiers, do your best not to kill civilians but recognize that mistakes are made.
And maybe that was the case in 2001-2002, but this has morphed into a sort of hazy nation-building / police-action kind of thing. But the tools and methods more suited to total war are still being employed, with the same brutal side-effects.
Minor nit-pick: total war is exactly about killing civilians. It is about the total mobilization of your nation's resources and assets--military and otherwise--in support of a violent enforcement of your political policies. Civilians are fair game, because they are assumed to be working in direct support of your opponents war-making capabilities.
That said, I submit that we were never engaged with an opponent capable of conducting meaningful total war against our nation, and as such any loss of civilian life is unjustifiable.
And maybe that was the case in 2001-2002, but this has morphed into a sort of hazy nation-building / police-action kind of thing. But the tools and methods more suited to total war are still being employed, with the same brutal side-effects.