My belief is that just as shisui tried to use his power to stop the coup, an Uchiha used his or her power to manipulate the clan and push them to start a rebellion. I believe it was Madara or Tobi. Think about it, in this chapter's flashback the masked man admitted carrying a grudge againts BOTH uchiha clan and leaf village. It's the perfect seed motivation for the scheme
The flashback said that if uchiha rebel, leaf will be in civil war and other nations/villages will pounce and strike; that's how a much greater war begins, a ninja world war. A ninja world war means likely use of bijuu. Masked man needs bijuu for moon's eye plan and he can maneuver in and out of the difficulties and intricacies with ease all the while picking the fruit of his labor with ease throughout the chaos and desperation of the ninja world.
I don't see any reason for the uchiha to stage a coup on their own volition given the third describing them as comrades; that's a will of fire style bond not easily broken unless a shisui level technique was used to instigate everything either generations before or what is more likely, just immediately
Prior to itachi's first discovery of the masked man. Uchiha are smart, no way the whole clan would sign onto a coup against their comrades.
It's also no coincidence that the only uchiha NOT agreeing with or participating in the coup are the strongest and most insightful. The only ones amazing enough to resist or go unaffected by masked man's manipulative jutsu/tech. I believe MS saved them. More on that later.
Ya, uchiha rebellion was a setup and i don't see evidence to show otherwise. The fact that a lone shisui was confident his sharingan could end a clanwide act of severe scale suggests a similarly powerful sharingan could have been used to move the entire clan onto a determined path.