I don't know if Itachi killed part of the clan with Tobi or not to be quite honest. I don't think Danzou did a thing that was hands on though. That's definitely not his style unless forced to. Just look at him in his limited actions. As a genin/chuunin froze up as volunteering to be the sacrifice when Hiruzen spoke up. Hid with ANBU ROOT during Nagato's invasion of Konoha to be in position for Hokage afterwards. Used Fu and Torune to fight Tobi rather than working with them. Took Karin hostage. These aren't the actions of a man of likes to get his hands dirty. Hell, that's partly why he founded ROOT in the first place.
I
definitely believe that we
don't know the whole truth about that night; thus, I agree with you on that point. I also agree that there's significance in Itachi basically telling Naruto to shut up about the Uchiha massacre (when ET Itachi and ET Nagato met KM Naruto and Bee) and just recently making Sasuke question what he accepts as "true" as Sasuke chased him through the trees on the way to Kabuto.
Further, if you do go back and read about what's been revealed, Kishi has done so in a way that it's
never definitive, given the source is Tobi (ultimate liar and manipulator of the Narutoverse) and how it's propagated. It's basically what Tobi said, and people
aside from Itachi confirming (Danzou seemingly does, but not definitively)/going along with to some degree (Naruto, Sasuke without a second thought - not sure how much Kakashi has accepted Tobi's words) Tobi's statement. I think that it's such a shocking "truth" with so much redemption behind it even if it is still Itachi killing, not murdering, his clan that people (e.g. Naruto, Sasuke) are easy to accept it who care about the two people involved, Sasuke and/or Itachi.
Granted, Kakashi cares, but he's much wiser, experienced, not so led by emotion, etc. that I think he's the only one who's heard "the truth" that hasn't decided if it's actually true, and he was the only one to not immediately accept "the truth" of Tobi's words. Further, he warned against propagating them. However, that's just speculation and possibly a bit off-topic. That's off the top of the head, so I could be missing someone like Kabuto. Kabuto may know something about the Uchiha massacre and try to screw with Sasuke and Itachi by starting to speak of that night if he gets more desperate (already tried to recruit Sasuke to backstab Itachi and join him..., kinda weak).
Essentially, this is all just fruit from a poisoned tree to use legal jargon, so it would be thrown out as testimony in court or the judge would at least instruct the jury on how to weight the information at the very least. This is a concept at least Kakashi understands.... Now, if it's verified, then it could be permissible, but that kind of makes me wonder if Tobi had Sasuke kill Danzou not just to improve his MS, satisfy some of his vengeance for Itachi, but to silence Danzou as a source of truth. Itachi was dead, Danzou would be dead by plan, and soon it would just be Tobi's word (he didn't foresee Kabuto and IWR obviously, let alone Sasuke meeting ET Itachi who broke his binding). After all, Danzou was not the type of ninja to talk about past missions (he condemned Itachi for thinking he even did so), so him fighting Sasuke was not much risk. Particularly given Sasuke's weak genjutsu (even Tsukiyomi), blind rage, and being lost in the darkness, amongst other factors. Sasuke could've still done plenty of damage to Konoha especially with Naruto, Kakashi, Danzou all gone and Tsunade in a coma. Sure, Nagato basically laid it to waste, but Sasuke could've potentially made the place unrecoverable and dealt with the two remaining elders along with a comatose Tsunade.
Danzou, however, was a potential information spout. Further, Sasuke accomplished virtually nothing at the Kage Summit as far as facing the 5 Kage. Wow, the Raikage lost his left hand for being a moron lost in passion of the battle and willingly plunging his arm into Sasuke's blaze release Ameratsu. As well, he almost died by Onooki's dust release if not for Tobi. Thus, I don't buy that Tobi actually hoped that Sasuke would accomplish anything at the Kage Summit except build up his MS, which he could've done against Konoha. Tobi could've shown up to declare war without Sasuke's sideshow, and it would have had the same impact. That's my view. Danzou, however, was a unique potential threat to Tobi's control over Sasuke if for some reason he said something, so he had Sasuke deal with him at a time when Sasuke would listen to virtually no one. Speculation of course.
My apologies, your OP led to my thinking a little too much (I'm actually holding back now, in part because I finished my cereal, lol.

), hence the length. Some times, the simplest stated ideas can form the basis for a much larger set of sophisticated ideas. I believe your OP and title, "Itachi did not kill the Uchiha Clan" perform that role elegantly for which I laud you. I think the importance of this post will grow in time when Itachi finally reveals "the truth" according to Itachi (sounds like a damn gospel at church, lol). Sure a lot of people on the forums can say, and have said that they felt the same belief as you did but didn't feel like typing it out, and that
may or may not be.
However, given that you put forward the time and effort in an effective manner, you are the publisher of this idea, which makes what you did novel while the rest of us are merely reviewers... Cheers! :izuna:
Peace