Kahuna, I'm no L5R expert, and I am summarizing what I do know here. With that caveat and apologies upfront for any error, let me tell you more. In the early history of Rokugan, the country was divided into clans. Each clan was given a job, and was exempted or given latitude in regard to customs and traditions when it was needed to make those jobs easier. For example, the Crab clan guards a wall which protects the country from The Shadowlands, a virtual Hell on Earth full of demons and corrupted creatures who would be happy to overrun the world. Since they live on the front lines, the Crabs are rough. They're loud, brash, uncouth and sometimes lacking in personal hygiene -- the half orcs of their world. If a Lion clan member behaved this way, they'd be social outcasts. But in a Crab, it's not only tolerated, it's some what expected. Now, with the Scorpions, it was determined early on that that in politics, situations get complicated, and there are times when necessity requires actions that no one wants to do or even have some one else do. For a historical example, early in the history of Hitler's rise to power, there was a failed assassination attempt on him involving a bomb planted in a briefcase. We generally disaprove of assassination, but we also generally agree that a lot of horrible things that happened in history might have been averted if that bomb had succeeded. Had Germany a Scorpion clan at the time, they'd have been the ones who planted that bomb.
As far a Jack, Nyarlathotep has got it pretty well decribed. It's pretty easy to call it when someone's choosing between good and evil, but as I said earlier, Jack's GM is a RB (sorry about the pizza milk), and his choices are seldom so clear-cut. Take for example, the oft-cited shooting of the wife's leg to get her husband to talk. Everyone's saying it's awful, and yes, they're right. In fact, it's even worse than that because what hasn't been brought up yet is that the woman was not just some stranger Jack was using as a pawn. He'd known her for years, and they were good friends. The shooting happened in her living room where Jack had been invited to sit down because it was so good to see an old friend after so many years. But just as it makes it worse that he shot a friend, it raises the point that he clearly didn't want to do it. Again, as mentioned earlier, the scenario provides a context that makes a difference. It wasn't a nuke in Yankee Stadium, but it was nerve gas and (if I recall correctly) at that point the location was the information Jack was looking for. Jack makes a lot of hard decisions, it's the thing that makes the show interesting. He once put a gun to a fellow agent's head and pulled the trigger to prove he was on the bad guy's side and not blow his cover. Turned out the gun was empty and it was all a test, but Jack was ready to kill the guy, I'm sure on the principle that if he didn't do it, they'd both be killed any way and the mission would fail. Oh yeah, one more complication -- the agent he had to shoot was also his daughter's boyfriend.
Back in the 70's Clint Eastwood played a character named Inspector Harry Callahan, nick-named "Dirty Harry". There was a lot of criticism of how violent that character was, but it always seemed to me that those critics all missed that Harry (especially in the earlier movies) had a real distaste for the violence he was so good at. There was a true sense of "why are you idiots making me do this to you?". I see the same in Jack. He loathes the kinds of things he does to get the job done, but when he sees that need, he doesn't hesitate for a moment. Jack certainly works with and is respected by people who are Lawful and/or Good. On Monday's episode, Aaron Peirce is bound to a chair, blood covering the lower half of his face and when offered a sweet deal for his silence, he looked into the face of the most powerful man in the world and said, basiclly, "I don't approve of anything you've said or done, and it is my job and my duty to see that you pay for all that you've done wrong and I will do that job and that duty to the best of my ability" -- that's paladin talk, and he supports Jack and trusts him implicitly.