After being turned Superman was used to snuff out the last remnants of his birth world, proving how far he's fallen.

After successfully getting Supergirl into Kandor, the surviving heroes informed her of the killing of all the Kandorians long before their arrival.

The loss of so many survivors of Krypton was already a tactical and emotional blow. However, the situation grew more painful upon the revelation that Superman had a hand in killing the Kandorians. 

 Having the last son of Krypton exterminate perhaps the largest pocket of survivors he ever saved is twisted beyond all measure.

 It shows how far the Man of Steel has fallen and just how depraved Nightwing has become as king of the vampires.

Strategically it makes sense. Nightwing moved quickly to eliminate or turn any power players that could threaten his new world order.

He turned Superman right away to use his powers for however long they would last and rob the heroes of a symbol to rally behind.

Atom's recounting of the attack on Kandor showed that Superman was among a team of heavy hitters sent to eliminate the Kandorians.