I'd say that's a perfectly fair assumption. Itachi was their man on the inside after all, I doubt he would have had them pull the trigger on the Uchiha if a coup wasn't imminent.
But of course, that's only an assumption we can make barring crazy ninja deception like someone intentionally framing the Uchiha somehow in order to get them wiped out etc, but it's pretty pointless to try and take those things into account.
Well, again, it being the ninja world basically removes other options.
It's not like you can just banish the clan, because then they'll go join another village, which will give that village an advantage over you.
You're assuming that "Mass murder for suspected treason" is even a crime to these people. It probably isn't.
Or that Naruto even HAS a court system. I've never seen one.