The song is indeed impressive, but the story is actually a bit questionable, as well as misleading. You see, I've played each and every one of the console Zelda games, and therefore have extended knowledge of the gerudo clan. I found you made the wrong assumption of thinking that part of the clan was made up of men, but in truth the entire race is made up of WOMEN. Ganondorf and the men before them are an extremely rare part of the race, so how could Shiek call a gerudo man if there's only one EVERY CENTURY?
Next, I have to state that the origins of Shiek are rather explanatory. We already both know that Shiek was Zelda's guise for the 7 years of darkness, however that name Shiek would never be used by the former clan she based herself on due to the fact they're called the SHIEKA. Shiek was just a hastily made name, a rather poor choice on the princess's account because I doubt that a member of the clan would be specifically named the same name as its own clan.
Finally, that war. Nobody knows what happened to the Shieka, so it's fair to make some fanfic, but framing the gerudos for the act seems a bit much; they're theives, not murderers. Especially not overthrowers. If anything, the alliance with the Shieka would've allowed them more men to get their children.
Love your songs, adore Saria's Wish, but this story just has too many plotholes to count. And besides, I'm already making a Shiek fanfic (taking place years after Spirit Tracks).