You know for a fact that Sarutobi wouldn't kill a clan? Even if that clan had put all of Konoha in danger for the chance to take over? Or if they had other plans in motion?
Honestly, the only "innocent" members of the Uchiha clan we have ever seen are:
-Sasuke's/Itachi's Mother (presumedly not born an Uchiha)
-Sasuke/Young (older brother style) Itachi
-Aunt and Uncle (who were such minor characters anyway. And the fact that they ran a bakery suggests that neither were very gifted shinobi)
And, just to point out, Madara said that the only ones that knew were Sarutobi, Danzou and the two elders. That could easily mean that the other three assigned the mission and Sarutobi found out later.
The fact of the matter is that there is a big gaping hole in the Sasuke/Itachi story that this "lie" fills a little too well.
When I first saw the two brothers together in the flash backs, my thoughts actually were, "How in the world could a brother that seems so caring all the time turn out so evil?"
Even his "final" act of defiance was interuppted by Sasuke's attempt to stop it.
Itachi's actions just don't add up on their own. Why did he lie to Sasuke when he did it? Why not just tell him that an order from his new master made him do it? We know that Madara helped, and that he taught Itachi the secrets of the Mangekyou Sharingan. Why would Itachi go to such lengths to make himself the sole focus of Sasuke's wrath? Even more importantly, why would he have let Sasuke live? And before you say, "for his eyes," consider something.
In their recent battle, Itachi is trying to take Sasuke's eyes, even though he hasn't awoken the Mangekyou Sharingan. If he didn't need Sasuke to awaken it, why in the world wouldn't he have just taken it from young Sasuke and keep himself from ever going blind in the first place? Why make Sasuke grow in strength?
If Itachi's main goal was to protect Sasuke, that makes sense. Maybe it was just me, but I predicted a chain of events similar to this way, way back. One of my Narunerd friends actually got mad at me last chapter because I am, "always right."
(I'm that guy who whispers in your ear twenty minutes into the movie how it will end, and am right 9/10 times.)
The, "I am the villain, gill me nowz!!!11!one!11!" thing just isn't stylish enough for Naruto. Think about it for a second. How many villains, in the grand scheme of things, have died being truly evil in the Naruto universe. Don't nearly all of them have a change of heart or back-story (usually regarding one they care about... or Naruto) in the end?
We have Haku/Zabuza, a variety of filler characters, that crazy guy with the bombs, Kabuto (though he is quite insane, and needs to stop acting cool when killing bees...), that other swordsman of the mist who has the little boy, Kimmimaru, etc.
No major villain (and most minor) have such one sided characters as "I want my brother's eyes so I killed my family."
It has to be something more. And it CLEARLY is.
Madara has NO reason to lie, especially considering the fact that the lie he is telling won't really help his position. Sasuke still knows that Madara is also responsible, and will not be joining him any time soon.