Danzö wasn't the only one with a problem against the Uchiha. As a matter of a fact, the whole of Konoha's high ranks were suspicious of them since the Nine-Tailed Demon Fox's Attack, because their Sharingan was the only thing capable of "controlling" the fox.
You suggested that Fugaku could convince The Third Hokage to take down Danzö, but that has absolutely no feasibility, since Danzö was one of Hiruzen's most trusted counselor and his loyalty to the village was demonstrably great. And also, Fugaku had no knowledge of Konoha's plan to wipe out the Uchiha, he just knew they were being segregated.
Obito also couldn't do anything beacause he didn't want to. You need to take into account that Obito, under Madara's strong influence, wanted to wipe out the Uchiha. Madara had a grudge against the current clan because he felt betrayed when they wanted to stop the battles against the Senju.
In the manga, Fugaku was the prime idealizer of the clans coup d'état, and wasn't just "going with" the majority of the clan. He also doesn't have the Mangekyö Sharingan, nor did anyone else besides Itachi and Shisui at that time. Well, Tobi had it, but he wasn't a de facto clan member at that point of the story anymore.
Now, the slaughter probably wasn't necessary to end the conflict with the Uchiha. Maybe not isolating them to a section of the village would be a better option, but that's speaking in real world terms. The manga (and by extension, the anime) shows the Uchiha clan as being cursed with hate. Their döjutsu is based on chakra mixed with hate, and based on those premisses, they were bound to be distrustful, angry and power hungry, so maybe there wasn't much of a choice.