I believe I read a discussion somewhere about improving the Amyro/Stingtail/Silence/Griff questline with some more options. I've never found it too bad, remember, you're on an island of prisoners and there are plenty of bad people around. You might even be a bad person yourself.
The magisters are essentially all working for the guys who put everyone on the island in the first place. The prisoners aren't going to care if you kill their guards, they might even be happy. Again, there is not really any reaction from them regardless if you kill all the magisters or not. This might be "missing content" or it might be the way the game will go.
DOS1 was like this too, you could murder everyone in the game and no one really cared. There are limits to the game system and how much effort Larian put into the ethics. Every event has to be scripted, might have bugs, etc. There is a lot of other stuff that will be deemed more important than how prisoners on the island react to mass murder.