I just have to point out that Cullen was VERY cognizant of Meredith's behavior.
Except that UNTIL The Last Straw, Meredith isn’t lashing out willy nilly.
Those blood mages she kept suspecting were everywhere? THEY WERE THERE. Orsino must be helping them keep secret! HE WAS. The Tranquil Solution? DON’T BE A NUTTER, ALRIK. You shouldn’t be shouting in the streets riling people up, Orsino. You shouldn’t remain neutral, your Eminence. SOMEONE MIGHT TAKE JUSTICE INTO THEIR OWN HANDS.
Cullen is greatly aware of all of Meredith’s comings and goings, and she never tightened her grip without cause. Unfortunately for most of the innocent mages involved, she cracked down just as hard on them as she did on ones that had actually done wrong. She wasn't mad with power. She was someone that took it upon herself to impose Order when she saw things were failing. The Viscount WAS useless.
He says in Act III that he seen the true face of madness and Meredith is not there. Fanatical and unforgiving, yes. But not mad. Not until Anders blew up the Chantry. The Chantry going up, the Champion, AND her Knight Commander turning on her AND THEN DISCOVERING SHE WAS RIGHT ABOUT EVERYTHING ALL ALONG broke her. The red lyrium might have had an affect on her, but if it was making her uber crazy go nuts she was hiding it very well. So, well, in fact, that a mage Hawke can stand across from her during The Last Straw and say that what Meredith does is WRONG and Meredith acknowledge Hawke's mage-y ness and point out that not every mage can carry that burden of their power as well as Hawke does.
It is why that I love Meredith as a villain. Everyone sets her up as this huge bad guy and so they do everything they can to subvert her and that turns her into the very thing they accused her of being.
TL;DR version: Meredith wasn't a blood crazed hell hound that Cullen was allowing to bite children. She was a capable, if overly stressed Knight Commander that was doing a difficult job in a difficult Circle in a tumultuous city and he was doing his best to support her. To make that job easier so that things wouldn't spin further out of control and make her crack down harder. (all his quest where he implores Hawke to take care of something before it becomes an official Templar matter)