"US authorities loudly questioned the methodology used in this study, but it is the same methodology used by the US Centers for Disease Control to estimate deaths from disease outbreak anywhere in the world, the same methodology the US and UK have always accepted in the past when counting deaths in nations where the American or British military are not directly involved."

This indicates exactly how foolish these people are.
The US and UK don't use a methodology- they are nations with many people in them and if referring to the govt, then there are differnent departments, for example with US you have State Dept, or CIA, or Defense Dept. As far as US Centers for Disease, if they use an difference in average mortality from a baseline before the disease in comparsion to period during an outbreak of a disease AND no other factors could contributing to these deaths than that could be a reasonable estimate.
With war in Iraq you have numerous factors which can cause the deaths of civilians other than US [or other coalition members] military use of force. First, you can have a change how you count and report the number deaths and in regards to Lance report, you can have bias and one is dependent of memory of people involved in the survey. [And this would normally not be the case in regards to Center of Disease type estimates.] But if Lance uses a strict methodology it can useful in predicting other conflicts if same methodology is used- is other words you would be comparing apples to apples.
Another factor is apparently Saddam released a large number of criminals prior to war. If any nation were to release most of their criminals from prison, you would see an increase in death by more murders being committed [regardless of whether there was a war going on]. More significant you have the terrorists/insurgents deliberablely killing innocent civilians and related to this is that the enemy does not wear a uniform nor have any way of distingishing itself from civilians- and therefore are counting as civilian deaths even though they are combatants in a war- and we are trying to kill or capture them. Another factor is that the period in which one is comparing to was a time in which Saddam secretly murdered hundreds of thousands of Iraqi and buried them is unmarked mass graves with family and friend uncertain of their fate [perhaps suspecting they were murdered but perhaps hoping they escaped from Iraq or held as prisoners.]

What can be said about Iraq war is that US forces have been lethal to the people who are our enemies and that in comparsion to any other war, innocent civilian deaths and killing friendly soldiers has been low- this has been largely due use of smart weapons, and enhance techology in gathering intel on enemy and knowing where civilian or friendly forces are in the battle space.