This is a great book. http://www.amazon.com/Lone-Survivor-Eyewitness-Account-Operation/dp/0316067598
I doubt any Navy Seal would regret joining. The camaraderie is intense within the Seals.
When I was in Fallujah with the Marines, the Seals were high-speed no joke good guys.
Did you read this book: Lone Survivor? Any thoughts about it?
This is a great book The first 3/4 of the book is all about training to be a seal and the last part is a story that will blow your mind. Good luck with Seal training.
There's always going to be that sense that the people around you, the people you know and spend time with are going to be important to you than complete strangers. It's an evolutionary trait; human beings, like most animals, are naturally inclined to place a priority on our pack/tribe/extended family/etc. Military training doesn't necessarily eliminate that - in some cases reinforces it because you are depending on the guys in your unit to watch your ass just like they're depending on you - but it does work to subdue a number of instinctive actions. One of the core fundamentals - if not the single most important one - of counter-insurgency strategies is to get the local populace to want to help you, not out of coercion or fear but out of trust. You do that by showing the community that your troops are willing to defend them from those who show no regard for the lives of their fellow countrymen.
The horrors of war doesn't justify things but it should be considered in the perspective. No one knows what combat will be life until they've been in it. There is no amount of training that can prepare an individual for that so when you have a group of young 18-22 year old guys facing the horrors of war for the first time, mistakes can be made. He's being shot at from an open window, he doesn't know if that house contains nothing but bad guys or if the shooter has his entire family next to him. He's standing at a vehicle checkpoint and one of the cars suddenly starts barreling toward him, he doesn't know if the guy just got impatient or has the car loaded with enough explosives to kill everyone in sight. Rules of engagement exist to give guidance during those situations where it's unsure whether you need to open fire to save yourself, your unit and the innocent civilians around you or whether you need to hold fire in order to avoid causing civilian casualties. It's a very fine line and when bullets are flying at you that decision doesn't get easier. You fall back on your training and we as a country have to ensure and hope that said training is sufficient to help him make the right choice.
But you're right that war crimes are never justified. Nothing can ever justify that. The soldiers who knowingly and willfully killed innocents deserve the harshest punishment possible. My concern is that people see those events and then anything remotely similar becomes a case of guilty until proven innocent.
Since you mentioned goat herder in Afghanistan I suggest you read the story of Marcus Luttrell and Operation Redwing. In 2005 his team was on a mission to capture a Taliban leader when they were discovered by some goat herders. Given the circumstances, the tactical decision was to kill them and continue on with their mission. They let them go and it ultimately resulted in the deaths of his entire team plus another dozen and a half that came to rescue him. He was eventually saved and protected by a local village. They put the lives of these civilians above their own even though all of the evidence points to those herders being the ones that ratted them out.
edit: sorry, forgot to link it
http://www.amazon.com/Lone-Survivor-Eyewitness-Account-Operation/dp/0316067598
If you're interested in seeing the mindset of people in combat then I recommend reading Generation Kill and One Bullet Away. The former was also turned into an HBO miniseries, the latter is by the platoon commander of the unit that Generation Kill focuses on. There are a wide variety of other books that can give you insight into what's happened in these wars the past ten years and what kind of person fights in them but those are first two that come to mind.
Everything I know about SEALs was from this book.
http://www.amazon.com/Lone-Survivor-Eyewitness-Account-Operation/dp/0316067598
http://www.amazon.com/Lone-Survivor-Eyewitness-Account-Operation/dp/0316067598
Very good read, once I started I couldn't put it down.