[apologies in advance for Wall o' text]
The real trouble with Cullen's role in the DA2 main storyline is that he is not the PC and is written such that he is influenced by the PC's actions. So, if someone is playing like a zealot for either side, he'll end up supporting some of those decisions in order to give you, the player, agency. I tend to think of it like the hardening process from DA:O, since he's so malleable. For example, I view the pro-templar moment when the three mages surrender as the moment where Hawke can decide if she's going to support full Annulment, or if she's still trying to save as many people as possible. That has to be her decision, not Cullen's. At that point, Cullen still needs that input and encouragement from Hawke to do the right thing. If Hawke asks to hear what he thinks, you can see how his perspective is different from Meredith's or even different from his own when he was in Ferelden. If Hawke chooses to spare the mages, Cullen tells his men to follow Hawke instead of Meredith and the mutiny in some sense begins. If Hawke does not, then he follows Meredith, as Pizza said.
Nevertheless, independent of the PC's choices, Cullen continually voices concerns and doubts about Meredith's path, telling the PC in Act 3 that he no longer knows if following Meredith is the same as following the Order. In the final moments of the Last Straw, he also voices concerns about neither side being in the right. So he is struggling with what is right, even if he needs Hawke to do anything active.
So, yes, he follows his duty and his superiors until the end, as far as what we see in-game. Some can fault him for this or also recognize how little he could really do before the end. He's not the hero of the story, Hawke is. So, defying Meredith earlier would have just removed him from the story... like Thrask et al., leaving no one from the "establishment" to side with Hawke and demonstrate the more moderate path in the end. i.e Gaider's "voice of sanity"
Finally, regardless of how hardcore the player makes him throughout the game, no matter what, he does stand up to Meredith in the end. And, not just because he's protecting Hawke, but because what Meredith's doing is not what the Order stands for in his view. So, like others have said, he's not the perfect character. He doesn't swoop in and save the day at the earliest opportunity. He's not the hero. He tries to follow his duty, and through the course of the game, I believe, his understanding of that duty evolves.
This is what I think makes him so interesting, and what's more, an interesting inclusion in the next game. Given his views on the Order, which side does he choose? Given his feeling that the Right of Annulment should be used only when all is lost... would he support full scale slaughter of all mages? Given that his whole life has been defined by duty, what does he do when that duty is gone or muddied? Since before DA2 came out they have been setting up the Templar Order for a shake up,
noting that the organization itself may need to change. Cullen is the perfect character to help explore this evolution, since his own path in some sense mirrors this.