Now, where would you get such a notion?
What the Republicans should have done is denied citizenship to former Confederates so they could not control the State Governments.
The fact that genocide would even come into your head shows the state of your own mind.
For once, I thoroughly agree with you. Southerners should have refused all contact with government, public life, and (insofar as possible) the tax man (which the distillers did anyway), and forbidden their children to vote, hold office, participate in public life, or volunteer for the military.
Massive passive resistance, in other words, like the Indian Congress Party.......who got independence in about 65 years, something like that. At the least, Southerners would have a) required the North to operate all levels of government, placing the federal theory and their own state governments at risk, b) required the Army to garrison the South, c) galled the North severely in one of the areas that drove Lincoln toward an emancipation policy, viz., his embarrassment at the existence of bond servitude in a free country, by requiring the North openly to rule the South in an imperial and despotic manner (think, "Ben Butler"); and finally d) required the federal government to make great exertions to collect the same amount of tax revenue they'd ordinarily have collected.
Before you scoff, show how the South would have been worse off under this arrangement.
Preconcession: The argument is made with hindsight and the benefit of the Indian experience in hand.