I like how people are only looking at the C'thun fight and trying to explain why Alliance has more kills then Horde on it.
In theory that fight is pretty equal to both.
But did you fail to see that you can't just enter AQ40 and start off by killing C'thun, you kinda have to kill a few bosses a long the way. And on most of those encounters allys have a huge advantage, giving more ally guilds the possibility to get to C'thun before horde does. Thus, statisitcly, seeing as there are over 2x more allys that are attempting C'thun then hordes, well, Allys should really have the advantage, shouldn't they?
Come back in 2-3 months when 20 guilds of each faction farms C'thun and start pulling statistics.