While you've definitely got a point there, the Biblical rationale behind the flood was that humankind had drifted so far away from godliness that He wanted to just hit the reset button and start from scratch. In contrast, the Mantids have been keeping the home fires burning for Y'Shaarj for longer than most races have existed. They even have a band of assassins in stasis whose sole purpose is to keep things the way the boss left them. Though granted, being based on a Lovecraftian type of entity, Y'Shaarj probably doesn't care much what the gnats do one way or the other. Or wouldn't, if he wasn't certifiably deceased.
The sha are byproducts of the Old Gods and Emperor Shao Hao's emotions, but don't seem to necessarily obey or work for them, they just do whatever they want. The Sha seem to be to the Old Gods what the Saurok are to the Mogu.
Hence, since they're not actually aligned with the old gods (and as a result are hurting the mantid by pushing them too hard), the Mantid oppose them.
You are now future Jack Noir.
Presently, you are trapped in a single moment, which increasingly feels like an eternity. Your boredom is surpassed only by your all consuming rage and contempt for existence itself.