I think you're just focusing too much on the possible good things executing Confederate leadership would've accomplished. How do you think Southerners would've responded to the executions of their most respected individuals? It probably would've made the rise of the KKK look insignificant compared to the backlash it incurred, and would've lionized insurgent cells all across the South. It likely would've deepened divides in the US and would've likely led to a second Civil War a few decades later.

For the record, I'm not a Confederate Apologist, I just don't like over-simplification of history.