Where this will hurt is in the United States? It will hurt in those parts of the world where there is is more concern for burned up Taliban than in the Moslem world. That's largely in the Western world, especially among some American politicians and pundits. How will this hurt? Congress can call for more "oversight" of U.S. military operations. The troops are already irked at the lawyers added to some staffs over the last decade. The lawyers are their to veto operations if there is too great a chance that the action will offend someone in the world and, ultimately, someone in Congress.
If the bodies were burned as a result of some psychological warfare operation, or just to clean up the battlefield, and the act offended the local Moslems, the troops will pay a higher price than any official investigation (which is already underway) can hand out. The troops have to deal with angry, and heavily armed, people every day. They try real hard to act in their own best interests. That being to avoid getting killed while carrying out their mission. Soldiers sent to Afghanistan go through many hours of cultural sensitivity training. They already know that one misstep can destroy lots of good will, and that in turn means fewer Afghans will pass on useful (often life saving) information, and more will fell inclined to take shot at Americans.
American troops in Afghanistan have conducted thousands of patrols, raids and fire fights in their pursuit of Islamic terrorists. Out in the mountains, the situation is often murky, and the troops are on their own. Decisions have to made on the spot to keep things moving. But there's a tendency, back in the U.S.A. to be unforgiving of anything that goes wrong, and to demand more micromanagement. In combat, things do go wrong, and more micromanagement causes more problems than it solves. But all this is nothing new, it started four decades ago in Vietnam. Apparently, an abundance of combat images served up on TV gave lots of pundits, voters and government officials the illusion they know what's really going on, and should get involved. The fact of the matter is that the U.S. military has been punishing troops for misbehavior since 1776. Yet all this means nothing to those who seek perfection, or simply another way to criticize the way the war is being fought, or the need for a war on terror at all. Any problems with the troops in Afghanistan are a lot closer to home.
On October 1st, an embedded Australian journalist filmed American paratroopers in Afghanistan burning the two bodies of two dead Taliban gunmen. Although the American soldiers said they were burning the bodies for sanitary reasons (they were starting to rot), the Australian journalist believed that, because there were psychological warfare troops in the area, this was all some kind of ploy to get some nearby Taliban to come out and fight. The media portrayed the incident as an accurate representation of what the Australian journalist thought he was witnessing, and a major defeat for the U.S. in their war on terror. Actually, stuff like this has no impact in the Islamic world. That's because, in the Islamic media, stories like this are invented daily. You can check out the English language sites for media in Islamic countries for examples. Some wild stuff there. The Moslems who hate us won't change their minds because of two burning bodies. Those Moslems who are down on Islamic terrorists won't get very upset about two of them getting torched, even though cremation is frowned upon in the Islamic world (even for Islamic terrorists who burn fellow Moslems to death in the course of their operations, which explains al Qaedas sagging poll numbers.)