Remember, we are talking about people who have lived their entire lives surrounded by religious propaganda. I'm sure we would have seen the same ruckus if this had happened, with reversed roles, in medieval Europe or in very Christian parts of the US. The whole idea of us being able to be there and trying to make Afghanistan a better place is built on actually having the moral high ground, and not being the same as the religious extremists who live there. That would inevitably only lead to more war(s).
I am not talking about ethics here since it's a lose-lose situation (like every other ethical problem) It's just a practical matter of them not being able to evolve since their status quo actively works against it. The only way to put an end to this it's through winning their hearts and minds; we already are relative and sympathetic to their view, it's time to shove ours down their throats until they see our way and can at the very least respect it without any flaring animosity. Heck I would be okay if they only stopped from pursuing their own Christians and women.
What do I care if somebody burns my flag (can't relate directly to someone burning the bible since I'm not part of any religious group...)? I don't know about you, but most of the Western world left behind the religious ignorance during the Age of Enlightenment and nationalist bigotry after the two great wars of the 20th century. This has allowed us to make scientific progress and to live in peace and harmony. If we want to spread these ideas to other countries the LAST thing we should do is to throw away everything we've learned and behave like barbarians ourselves!
It's precisely because we are not rioting when they burn our flags that the differences in our culture are evident, even the post 9/11 incidents of anti Muslim sentiment can't really compare to theirs. If we were able to actually converse and acknowledge when others are right despite any fundamental differences or how shattering it may be to our mental frames, then there would be no need for war. But as they will not; by their own volition, change then it is up to us to educate them. Throughout history the only way to do this was for the weaker culture to be absorbed into the greater one, because of American culture has spread through globalization it is a half won war. The only thing remaining is sending the right message and repress any unrest it may cause.
Sadly, in the current state we are sending the worst scum imaginable - people desecrating corpses, killing innocents and posing with SS flags. It's like a situation from "1984". We sent soldiers with the (dubious) mission to protect us from terror - yet their very presence, because of incidents such as these, is the single greatest reason for terrorists to fight in the first place! It's a vicious circle. And the only way ever out of it is through compassion and understanding.
You know from listening to you I get the feeling that you haven't seen this side of war too much. All wars go through this and this one is no exception, the mental exhaustion coupled with the stress and lack of leadership (or the wrong kind) will ultimately result in insubordination. Which when the flight or fight response its an all time high translates to the usual events.
What they actually teach you to cope with taking a human life is to dehumanize them, what they don't teach you it's how to remain human.