What I got from it is this:>sometimes you have to make a tough decision between what you want and what is right>you might love someone, but sometimes you have to let go to save the lives of others
I didn't see any real anti war/anti authoritarian message, I just saw the necessary violence that had to be used to keep the general public safe. The Sect didn't care about the safety of the people they were hiding amongst, and the Wolf Brigade clearly was trying to avoid unnecessary kills. In the end, they had to play dirty to protect the innocent that they were put in charge of.
This story is a tragedy, meant to show that violence is sometimes necessary for the greater good.