I don't understand why this has your collective panties in a bunch. There are other historical inaccuracies within the CIV universe, and other nonsensical things as well.
Such as...
Why are we allowed to play as the Americans in 4000 BC? We Americans didn't exist until well into the AD years.
Why does building the Pyramids put a granary in all your cities? Just what do the pyramids have to do with food storage?
How is that ANY of the leaders of whatever Civ you choose to play could be the leaders back in 4000 AD all the way through their exisitence?
Very simply, some licence needs to be taken during the creation of a game. In the case of the Iroqouis, just think of them as the collective Native American tribes, as the description from Firaxis says they are. Ok, so the American Indians aren't supposed to get horses until the settlers introduce them, but once they do, the Mounted Warrior was a part of the American Indian culture. So Firaxis has taken a little bit of a license by letting them have the Mounted Warrior a little earlier, (but only if they have access to horses). I say, so what?
They have not introduced a unit that never existed, and in terms of gameplay balance, they have probably determined that the Mounted Warrior gives the Iroqouis what they need in order to remain competitive in the game.
Most of the games that I play are on random maps anyway, so the historical inaccuracy of having horses earlier will be much more likely to happen anyway. By the same token, it's equally likely that if I play as the Romans, I might not gain access to Iron until much later in history than they really did and will never be able to build Legions during the historically accurate time.
The point is, if every game you played were simply an exercise in recreating history as it was, then the game would get boring quickly, don't you think?
Just my two cents.