The Gem Empire has probably existed for millions, or billions of years. Considering that gems do have free will (even if they are born loyal), it seems statistically improbable to me that the Crystal Gems are the first rebellion.
And to deal with the rebellions, they sure had to be strong enough to defeat at least eight gems.
About the "free will doesn't mean shit" argument:
You can't really rise up against the human elites. At least not easily. The gems, however, are literally born with weapons, which have been proven to be quite effective against the Diamonds. But as I explained in the first paragraph, they shouldn't be able to do batshit.