Now I kind of want my first gal to be, not exactly anti-mage, but afraid of them - until she ends up with a glowy green fade hand. So then she's conflicted, just like Cullen 
My character is a mage... who is hyper-aware of the dangers facing mages, and thus will be terrified when she ends up with a glowing souvenir of her unwanted trip to the Fade.
Her glowy hand will make her fearful and ashamed, poor dear.
I don't think Cullen from Origins or Da2 would let the raping of innocents go. I can only assume he didn't know about it or had too much misplaced faith in his superiors that he wrote off any rumors as absurd. He may have even privately checked into it and found nothing. (Through cover-up, fear, or bribery)
I think this is the most likely. I just don't think it fits with Cullen's character to have known or had concrete suspicions and done nothing. He's a decent human being with a pretty strong moral compass (even if it doesn't always quite point in the right direction, he tries) and he seems to have pretty deep religious faith, so I can't see him being indifferent to something that he'd likely see as both a crime and a sin. He has an extremely strong sense of duty, and I can't see him shirking that duty by deliberately failing to protect the people he is tasked with guarding. And to be blunt, at least at the start of DA2 he has sufficient fear of mages that it wouldn't even make sense for him to permit physically intimate close contact between his men and them.
My guess is that the perpetrators deliberately kept Cullen in the dark, and the victims didn't feel they could tell him what was going on.
Abusers can be really, really good at hiding their crimes. And unfortunately, abuse is the scourge of any sort of residential care setting. Honestly, you would not necessary know what was going on, trust me on that. 
So, Anarchy, or the S.O.S.? I hope there's room for Reform in there. Somewhere.
Yeah, that's where my Inquisitor would lean. She thinks there's a lot wrong with the status quo, but just burning it down and starting over is kind of counterproductive in terms of helping people, because a lot of innocents get caught in the crossfire. When possible she'd choose reform over either chaos or stagnation.
My own headcanon is that he doesn't know right away. And by the time he does, it still takes a few more 'straws' for him. He is in the Gallows courtyard when Mer tells the mages to prepare. And he says nothing.
I agree, and I also tend to wonder exactly how and what Cullen was told when he did find out. Since he wasn't there when it happened, the story he got could have been a pretty skewed version of the truth that made Meredith's view seem more reasonable.