The village suppressed the Uchihas because they were cursed by the Cycle of Hatred. Only Itachi and Shisui didn't fall for this curse. So it was better to wipe them out because they would do the coup d'tet at any cost.Maybe the clan wouldn't die if they had support from the people but no lets just be on the side of the fascist country who has been opressing the Uchihas for years... how can you see doing this good?