I agree. The Japanese society doesn't need it to protect itself from within; that's what Sibyl is for; but to protect themselves from without; i.e. from the other foreign nations. The drones are used as border controls. In the episode with the riots, Division 1 said that it needed to reprogram the border drones to control the riots.
I think I understand what you hate about it actually: Makishima himself. I mean like you said, if Makishima didn't come
you wouldn't know all this things about Sibyl and would've just be as happy as most people in PP-Japan. I think in the next 2 episodes Gen will tell the story of why Makishima is doing all this, but for now it looks like the typical anarchist. He said so himself actually why he's dong all this: in this world of sugar-coated tyranny, he want to see what will people on the edge do when they are given a real choice to make. He does it for that hikikomori dude that plays around in anarchists' forums things. He gave that female student artist the freedom to express herself more fully. The biggest one, I think, was he gave Akane real power to judge someone by giving her a shotgun to stop him from killing Yuki. He is, for all intents and purposes, Chaos; just want to see the world burn. He said that too when Sibyl offered him to join them.
Now on to Sibyl's flaws. I would like to think that I know how Gen thinks with this. Since I am assuming that Makishima, for now, it just Chaos, and as you said that Sibyl is Order; a perfect one to all eyes; he just want to see how the populace will react. And in all that effort, we know that Sibyl is as flawed as humans are, since they are essentially still human. In a sense, this is like "bring down the Big Brother" thing, only the populace is actually happy for once, and the rebel is just some psychopath.
I feel like the show, looking relatively in its universe/timeline, is showing how Sibyl usually deals with psychopaths that it can't judge through cymatic scan, and failing. Usually all those psychopaths agree on Sibyl's offer, but this one time it's someone like Makishima, a, so far and dare I say, chaotic neutral. He is the
MacGuffin to show how flawed is Sibyl is.