You could say that about a lot of modern real jobs that still exist. I remember the History Channel documentary about the War on Drugs. A former CIA lady was on there and talked about how the CIA's goals didn't align with the DEA's, and she "would do anything to protect the United States." Who knows what she and other CIA agents have done. But we know the lives the War on Drugs destroyed, and outright ended. Most of these people live to a ripe old age in obscurity.
That, and like the agents I mentioned, these ninjas thought they were fighting for a just cause.
Depends on how the death is handled. This one felt cheap and forced, like overkill. Reminds me of some of the deaths that happened at the end of FMA: Brotherhood, because reasons, just to add the body count and make the final battle feel more impactful, but most of them felt very forced.
If anything, it has felt like Higan has a higher chance of going down in a blaze of glory (I guess that could still happen.)