I am slightly frustrated that everyone goes on about 'Kirkwall' but never mention the complicit knight Captain who is now in charge of the largest up and coming military force in Southern Thedas. It just sounds like a missed opportunity from all the Inquisitions enemies, that could have been one hell of a smear campaign, but they don't even try. You're letting me down again, Corypheus/chantry/evil templars etc.
Although, a thought just occurred to me. The Seekers police the Templars right? Why did no Seekers ever check out Kirkwall, or did they take a look and decide it was all good as gold? Sending Leliana to investigate instead seems silly. I ask only out of curiosity, because I imagine many a Hawke would have some choice words for Cassandra if they had a chat.
I think Cass actually discusses this in a banter? She briefly mentions that the Seekers checked out Kirkwall, but it was before things got really bad, and they decided that Meredith was harsh but not over the line. Which IMO means they either 1) didn't look very hard on purpose or 2) sent the world's dumbest Seeker to Kirkwall.
It's a bit handwave-y, TBH. My personal headcanon is that Kirkwall is the templar stronghold of the Marches, so its templars have more resources to push back against external intervention. Bribes, political pressure, calling in favors, whatever they needed to make sure Kirkwall "passed" Seeker scrutiny. It probably helped that Elthina is fairly useless 
Meredith owns and controls Kirkwall essentially. She is the one that put the last Viscount into power. It is her city. They make this evident in the opening scene when Hawke wants to get into the city and the captain basically says I'd prefer not to have the Knight Commander after my head, I don't care how pretty you are. Why would a Templar have any control over refugees entering the city? This should be a city issue and fall under the office of the Viscount. TWOT2 explains that she elevated the current Viscount, and she pretty much as say over everything. I would imagine a Seeker wouldn't find anyone willing to speak up out of fear.
Cullen, oh poor vilified Cullen. Not that I find him blameless but lets look at his life, at 13 he went into the Chantry with rose colored glasses. The Templar's are the protectors of the weak and helpless. He is going to be a knight in shining armor making all things right with the world. And then they spend the next 5 years brain washing him. (Here is where I have great respect for Alastair, due to his bitterness of being abandoned he refuses to accept their doctrine, but Cullen laps it up like a puppy.) Then the boy is subjected to the lyrium leash, if he had any reservations it's too late now. They own him. He soon sees what happens to older Templar's but he is bound by duty and honor to follow the doctrine they have hammered into his head. He follows blindly under the delusion that this is the right way. There is no room for questions even when he knows in his gut something isn't right, he is a soldier, and he follows orders without question.
Tortured by demons and watching the circle fall to blood mages is pretty ****** traumatic. It reinforces the Chantry's indoctrination that mages are evil and must be controlled. I don't blame him for his rants in the circle quest in DA:O, we often say things in anger we wish we could take back later. But this experience hardens him and he throws himself into his job fully now, all reservations are gone. He's sent to Kirkwall, where his Knight-Commander uses his fears and his trauma to manipulate him, makes him her second in command, but still leaves him in the dark on many of her decisions. Actions she knows he would be against.
The first letter he receives from his sister is mentioned in DA:I as his turning point back to humanity. He starts letting go of the hate and is slowly becoming that boy that wanted to be a Templar to help people. But his commander holds a strong arm over mages and templars. Mages are made tranquil and tempalrs are tossed out on the street for minor offenses. Here is where I see him at his weakest. He is afraid to trust his own judgement, so he does nothing, or next to nothing, but he is beginning to think that there has to be a better way. In the end he finally comes almost full circle. He stands up to the tyrant and defends Hawke no matter what position they took, and after strives to rebuild and make Kirkwall safer. If the red lyrium hadn't been an issue he may have succeeded.
The Cullen that we meet has had a year to come to terms with the man he was and is striving to be a man he wants to be. In the final scene he thanks the Inquisitor for giving him a chance to redeem himself, he doubts he would have done the same to someone in his similar situation. He's deeply flawed and he knows it. The whole game is a struggle for him to put aside the monster and forgive himself. If he succeeds he's goes on to help Templars, if he doesn't he dies of Lyrium addiction. But no man can do it alone, only with the support and friendship of the Inquisitor is he truly saved.
Er wow, that got a bit longer than I intended. 