No it would have made it worse for Blacks in the south because it would have made the bullshit that's till going on today with White people in the south even worse. The South already has something of a martyr culture. What you're suggesting would have kicked it up several degrees.
You might have noticed I called reconstruction a failure. That isn't because it failed the white southerners; it's because it failed the black ones. All what you're suggesting would have done is made southern whites feel further valorized. Counterfactuals are hard, but I fail to see one where that would have somehow made things better for black people instead of worse.
What exactly would executing them have accomplished besides making White southerners even more likely to retaliate?
Let's move away from the anachronism and actually look at what people were saying and thinking at the time. Reconstruction could have worked. Ultimately it didn't, but the US had no way of knowing that. What they realized is that making martyrs out of the Confederate leaders wasn't exactly going to help their chances.
Shooting all the Nazis after WWII and making it illegal to even sing their national anthem actually seemed like a super effective way to stamp out white supremacy in Germany. I tend to think the reason the Confederates viewed themselves as wronged martyrs is that we left all the Confederates alive to teach their kids they were right all along. If we'd hung them all and banned all Confederates from serving in public office, as Grant wanted to do, maybe Reconstruction could've actually worked.