And Danzo is not a well-intentioned extremist. The manga made it pretty clear he resented Sarutobi for acting when he couldn't which resulted in Sarutobi become Hokage. Danzo's problem is he thinks that his own personal desire for power and his desire to protect Konoha are one in the same. Did you forge this well intentioned man murdered Kosuke to prevent Naruto returning during the Pain invasion and then had his Root goons stanby while Pain attacked because he wanted the murder and mayhem to result in people losing faith in Tsunade? Like I said, sure he wanted to protect Konoha but he was not well-intentioned because well-intentioned would mean putting Konoha above his own personal goals and he couldn't do that because he thought they were one in the same.
Having said that, I acknowledge it is a possibility (notice how I don't totally shoot it down as impossible) but simply think it is unlikely given Obito's power levels. I mean hell what is preventing him from using the Zetsu to help him do the deed as I am pretty sure they were around then? Look, you don't have to agree but to try and pretend like it is impossible for one of the best ninja's in the ninja world with access to all of Madara's knowlege and Akatsuki to boot to murder the Uchiha quietly is just you being stubborn when we know Itachi and Obito did it and there is no indication in the story that Obito had to exert himself tremendously to do so.