There's no way the Uchiha Massacre isn't an inside job in MfD. The alternative is that a single teenager murdered all combat-ready ninja in a clan, alone, and without the rest of the village noticing. Either Itachi had help from Leaf ANBU and approval from Hiruzen, or he's an innocent who managed to escape the massacre, making himself into a convenient scapegoat.
I mean, in Naruto canon Itachi had help from a godlike ninja who had space-time bullshit powers and a Danzo-orchestrated conspiracy to at least keep the rest of the village looking the other way. Quoting Narutopedia:
In a single night, Itachi and Tobi slaughtered the entire Uchiha clan. In the anime, Tobi slaughtered the military portion of the Uchiha Clan by directly attacking the Konoha Military Police Force headquarters, enabling Itachi to slaughter the civilian portion without much resistance.
Even Kishimoto made sure the fix was in and that Itachi did the "easy part".