I know Tobirama would be against it, but would a successful coup be a bad thing for the village? If Danzo and ROOT die the village loses the cause of all it's problems. If the Uchiha die the village loses four present and upcoming S-Ranks (Tobirama, Shisui, Itachi and Sasuke) plus uncounted Jounin and other ranks. The village only has a handful of top ranked ninja, I'd say four or five now (Hiruzen, Kakashi, Jiraiya, and Gai, Tsunade on a good day) and two or three upcoming (Naruto, Sakura and Konohamaru).
If we have to fight a civil war that opens the village up to attack it's a bad thing. If we have to kill less than four of our top guys a successful coup is a net benefit compared to canon. Hell a targeted series of assassinations could be acceptable. Sarutobi didn't approve but he never acted against Danzo for what he did, maybe the opposite is also true?