holy necro... I just got blind sided by such an old thread.
Varian (like Garrosh) is only an excuse to keep the Alliance fighting the Horde to the very extreme, as the game intends. Now, Blizz has to keep the lore balanced: they can't make one faction be right about its actions and the other one wrong. And what's the easiest way of solving this? Just throw in a couple of hot-headed characters and make them leaders of their respective factions. Not the most creative thing to do, but hey, it's just a videogame. The story here is just a by-product.