You really can’t have an argument that isn’t somehow based on the concept that black people are dangerous, unclean, uneducated, incompetent or inferior to white people and that they’d infect and annoy white people and harm civilization with these habits if desegregation occured.
Why not look at some of the arguments that the educated class are making against gay marriage for a good comparison to the kinds of arguments you are looking for for segregation. Most aren’t that good and would fall apart in a high school debate club. I honestly doubt there are many good arguments.
William F Buckley was an intellectual who died recently who defended segregation (he also defended Franco and fascism too).
“The central question that emerges … is whether the White community in the South is entitled to take such measures as are necessary to prevail, politically and culturally, in areas in which it does not prevail numerically? The sobering answer is Yes – the White community is so entitled because, for the time being, it is the advanced race. It is not easy, and it is unpleasant, to adduce statistics evidencing the cultural superiority of White over Negro: but it is a fact that obtrudes, one that cannot be hidden by ever-so-busy egalitarians and anthropologists.”
“National Review believes that the South’s premises are correct. … It is more important for the community, anywhere in the world, to affirm and live by civilized standards, than to bow to the demands of the numerical majority.”
“The South confronts one grave moral challenge. It must not exploit the fact of Negro backwardness to preserve the Negro as a servile class. … Let the South never permit itself to do this. So long as it is merely asserting the right to impose superior mores for whatever period it takes to effect a genuine cultural equality between the races, and so long as it does so by humane and charitable means, the South is in step with civilization, as is the Congress that permits it to function.”
Basically he is saying white people are naturally smarter and more responsible than black people and white people shouldn’t use their innate superiority to exploit black people, but they should keep them from voting or having any power since they’d just screw everything up. And Buckley is considered one of the greatest intellectuals of modern conservatism.
The only semi-valid argument that some black leaders were endorsing was that desegregation would backfire and make the races hate each other even more, and that it was best to either remain segregated or slowly integrate (rather than do it quickly).
Malcolm X (up until near his death) supported segregation. And WEB Dubois felt it was better to slowly change attitudes on segregation.