Where is the justice for every blood thrall in Tevinter? Where is the justice for all the people the Qunari mind erased?
It is all within the same place: nowhere.
Where is the justice for every Templar struck down by mage for simply doing his duty? Where is the Justice for every person slain by a rampaging abomination, when the locals go "Oh well...its like if your house fell in." Where is the justice for all the innocents harmed by magic, themselves included?
If you want an arbitrary concept like 'justice' to be upheld you need to look at the root cause itself.
Human nature.
The issue with your examples in comparison to the mage/templar dilemma in the Circles is really straightforward.
The Qunari and the Imperium are entire societies. Yes, there should be justice for the people oppressed, but their laws in their societies, while are not right, make their actions legal, agree with them or not, and I don't agree with them at all.
In the case of the Circle's and how mages and templars get along, there are written laws given by the Chantry that are meant to protect mages and the templars are supposed to uphold them, and the Seekers are supposed to root out corruption from within the chantry and the templars.
But the real issue is that the templars, especially in Kirkwall, are deliberately breaking Chantry law and are abusing their authority over mages, and the Seekers under Lambert, and possibly before him, are ignoring their own duties in favor of an ideology and are deliberately overlooking corruption and turning the other way.
When a law is set, there are consequences for breaking it, consequences that are meant to discourage others from breaking that law as well. But when the rules are not enforced, the consequences and the punishments never come, then the system fails.
The Circle's purpose is designed to protect mages from the world, but also to protect the world from the dangers of magic.
Just because Tevinter has slaves and blood magic, the Qunari have removed all concept of free will and choice does not mean I can't stand up for the people abused by any system. It just so happens that this thread is about mages and magic, so I will point out that the templars have failed their mandate to protect mages and protect the world, and the system that they fought to uphold is inherently flawed.
Not that it matters really, since Cassandra, Vivienne or Leliana each address the issue with the Circle's in each gamer's individual playthrough and players can choose which path they want to take.