I felt it was more like he wanted to follow Louisoix's goals without understanding his mission. Alphinaud wanted to protect and uplift Eorzea, but didn't bother to actually understand it or its people. He just thought he could throw his high-minded ideals around and everyone would immediately fall into line behind him and make the world better. The world doesn't work like that, and it took his own initiative spectacularly backfiring on him (the Crystal Braves) for it to start to sink in.

Kind of makes him a foil for Gaius, now that I think about it. Both of them sought to impose their own ideals, but Alphinaud tried to be diplomatic (or at least, he thought he was trying to be), while Gaius went for overwhelming military power. Both failed because they continually underestimate the people they're trying to control.