Alistair isn't exactly anti-hero friendly and I don't think he's meant to be.
But here's the thing about Alistair and the typical Grey Warden mentality, morality wise, he's Good-Neutral. He's not beholden to the law or to chaos, which means that he won't condone cruel or morally questionable actions and attitudes even when necessary or when the results outweigh the cost.
I typically play Good characters and get along with him rather well, though my evil mage pretty much made him into a chew toy(If I hadn't erased that save, Amell would've recruited Loghain, put Anora on the throne and got Alistair executed out of pure spite and fun). But when it comes to Redcliffe, I often use the Blood Magic Ritual because I play as a character whose in a hurry to save Connor. I can convince Alistair that I had to do it (realistically, going all the way to the Circle would've left too much time for the demon to regroup and kill everyone) and though he'll reluctantly agree, he'll make it clear that he doesn't like it.
He's meant to be the "moral" signpost in the group, the guy whose meant to keep a more morally-loose warden honest and call them out on any questionable actions that they commit. Not exactly in line with Warden thinking, but he was a novice warden so some of the mentality hadn't sunk in. Alistair saw his fellow wardens as family and I don't believe he had been in the order long enough to really understand what it meant to be a warden beyond Duncan's words. Then again, Duncan recruit Alistair because of his determination, his character and his loyal heart. Being a templar was also a good bonus.
The fact that Alistair was recruited based mostly on his moral character says something about Duncan's judgement and for Grey Warden standards. There is a place for "moral" signposts in the order, to keep the order honest and maintain it's integrity.
I personally hate how hardened Alistair will outright abandon you if you recruit Loghain, but from his standpoint it's understandable. Loghain is the last person that should be recruited in the order after all of the damage that he did to Ferelden and to the Grey Wardens. Let's face it, the only reason that Loghain was recruited was desperation for an ambiguous reason that Riorden just assumed that the Warden knew. Recruiting Loghain to Alistair is the ultimate betrayal to the other wardens as Ostagar and the fact that he's recruited as a "punishment" cheapens their sacrifice and the honor that being a warden entails.
In D+D, good guys rarely work with bad guys for a reason. And there are some things that can be done in Origins that are pretty much synonymous with evil (Defiling the remains of a holy figure, Many opportunities for unprovoked violent murder, Putting Bhelen on the throne, Sicking the werewolves on the dalish clan for something that their leader did, Indiscriminately murdering every mage in the Circle Tower even if they're not abominations or blood mages, and taking a bribe from Vaughen to allow him and his men to gang rape your cousin along with other elven women who were meant to be your maids of honor (Please tell me most players killed that sob))