Ny difference between “captured” and killed XCom operatives

The mission reward for VIP capture missions is both supply and intel.

If you kill the VIP, you get the supply reward, but no intel.

If you capture the VIP by knocking them out and carrying them to the extraction zone, you will get both the intel and the supply reward. You will see them on the mission loot summary screen with their hands tied behind their back, and they do not appear very interested in joining your cause. Then you will never see them again.

There is an achievement¹:

Heroes of the Resistance

Beat a Retaliation mission with less than 3 civilian deaths.

Otherwise, as long as you manage to save at least 6, I couldn't identify any difference in the outcome. There are no rewards for Retaliation missions, so there's no difference there.

You are offered a cache of supplies/intel/materials by the Resistance after completing a Retaliation mission, and it's possible that differs based on how many civilians you save, but if it does, I couldn't detect it at all. I also looked through the XCOM 2 source released with the mod tools, and there doesn't appear to be any different treatment for Retaliation missions compared to any other type.

_{1: According to skully, the achievement unlocks from less than 4 civilian deaths, in contradiction to its text. I was also able to confirm this in the XCOM 2 source.}