The real problem was that if the Uchiha rebelled, it would weaken Konoha greatly. At a minimum, they would lose the majority of the Uchiha clan, which in themself are a large part of Konoha's power. The balance of strength between the Great Nations was always critical; if one of them dipped too much in power, others would start war to prey on that weakness.
Ultimately, this was all "plot" once again; Kishi gets a bit half-assed sometimes. The threat of a large-scale war, rather than merely a civil war, makes the situation somewhat more believable in this case.
Now if only Kishi had explained the Uzumaki Clan's fate, or the Senju Clan's. These would have been good subjects for a filler arc, unlike all of the worthless, non-cannon fillers we've gotten. The series has more loose-ends, and more fillers, than any other, and yet it can't use those two issues in a satisfying way.
