Uhm... There is no criminal justice system in dragon age (and if there were we players and Hawke are hardly objective enought to ever pass judgement) and the criminal justice system isn't 'just' it is necessary.
But there is a city guard meant to enforce the laws. Granted, I see more corruption there with the old Captain of the Guard and the templars trying to force Aveline out so they can consolidate their power.
But the point I'm making is, even if Meredith won't hold her templars accountable for their actions, even if Elthina doesn't hold Meredith accountable for hers (taking power far beyond that of Knight-Commander. Refusing the city access to the Viscount seat, etc...) I can still hold Anders and those I'm associated accountable for theirs. If they commit a crime, then they must be held accountable. If they want redemption, then they need to not only own up to the crime, but make amends to all those they wronged. If they are not willing to do that, then the heavy hand of justice must fall on them, according to the crime committed.
That's my view. I kill Anders because he kills so many people and wanted to urge Meredith to call a Right of Annulment. He wanted to remove any chance of compromise. He takes accountability for it, but he still wants the war. He doesn't want to apologize and make up for it. Because he killed so many in the Chantry, death is the appropriate response. It is justice.
Did I support the cause? Yeah. Did I support the action? Not really. If the templars struck the first blow, no one would question the need for reformation. If it was the Circle, there would likely be more people in the Templar's camp. But it was an apostate, acting on his own. The blame falls solely on his head.
The Right of Annulment falls on Meredith's head, and the templar rebellion falls on every individual templar who refuses to back down from dominion over mages. And mages are responsible for their own actions.
If there is no criminal justice system, it's because people blatantly favor one group over another, making unfair situations. Vaughn in the City Elf Origin most certainly deserved being inprisoned and possibly castrated, but even after so long in prison (for the wrong reasons) he has absolutely no remorse and is still very much anti-elf. Only he would be the Arl if released. Who would hold him accountable?
I can't change the world to fit my view, but I can give myself a single standard, and live up to it.