Alistair was pretty much always pro-mage. He's not afraid of or repulsed by magic in the least. If anything, he's fascinated by it, and in DA:O the gifts that will get you the best returns from him are magical artifacts. Plus, it's pretty clear from his stories about his childhood that he has little love for the Chantry or the Templar order.
People read him as anti-mage because they think he hates Morrigan, based on their in-party interactions. But I always thought that interpretation was way off base. I mean, their "conflict" basically goes:
"You're dumb!"
"Oh yeah? Well, you have a big nose!"
That is like, second-grade level garbage right there. It's borderline flirting. If anything, I was expecting them to bang.