The following contains spoilers for Action Comics #1046, on sale now from DC Comics.
Superman's Warworld mission has become about more than just freeing the planet and unseating its tyrannical dictator, Mongul. The entire "Warworld Saga" has become about the eternal fight of good versus evil, with Superman and Mongul representing the epitome of each of these ideals. There's no question that the Man of Steel is pure of heart, however, the way that Action Comics highlighted that proved that the hero's darkest moment has been erased from continuity.
On his quest to retrieve the all-powerful Fire of Olgrun, Superman came face to face with the Fire's ethereal guardian in Action Comics #1046 (by Phillip Kennedy Johnson, Fico Ossio, Lee Loughridge and Dave Sharpe). She was surprised to look at the Man of Steel, seeing his entire life and accomplishments, and find that he had made it to this point without killing a single person. Although this seems like an obvious observation, as it's Superman after all, it actually reveals that the Man of Steel's most harrowing moment is no longer part of continuity.
The moment in Man of Steel when Superman killed Zod was controversial. What most people don't know is that the hero was in a similar situation in the comics - but it was even worse than the feature film. In 1988, Superman traveled to a pocket dimension that contained a world not dissimilar to the DC Universe. In that world, a version of Lex Luthor released General Zod and his allies Quex-Ul and Zaora. They proceeded to commit genocide, laying waste to that Earth. They had planned to do the same to Superman's own Earth and would stop at nothing until they had done just that.
In the final issue of the arc, Superman #22 (by John Byrne, Petra Scotese and John Costanza), Superman decided that there was only one way to stop them and took it upon himself to be their judge, jury, and executioner. He stripped them of their powers using Gold Kryptonite. Then, he, personally, exposed them to Green Kryptonite. Although they begged for their lives, the Man of Steel wouldn't stop and continued on until the Kryptonite finally ended their lives. This was a pretty harrowing and impactful moment. Superman has had a no-kill rule since the very beginning only for it to be broken on the character's fiftieth anniversary.
It wasn't something that came and went either. His execution of the three Kryptonian criminals had a major effect on him in the comics that proceeded it. He had a nervous breakdown not long after and, for a short time, became the hero Gangbuster. He then went into a self-imposed exile, venturing out into space to discover whether or not he was worthy of even being Superman anymore. Oddly enough, this ended with his first post-Crisis encounter with Mongul, in which he freed Warworld and deposed the tyrant, just as he plans to do in Action Comics today.
Although it may have been an alternate reality version of Zod, it was still murder. As well as that, it had a profound effect on the character, and the effects of that act continued on well after Superman #22. Even still, the fact that it affected the Man of Steel to the point of a psychotic break says a lot. It was wildly out of character back then, and it still feels that way even now. Although both Henry Cavill and Christopher Reeve's Supermen killed (or seemed to kill) Zod, both were put in positions where they had little choice. The Superman from the could have simply stopped with the Gold Kryptonite, leaving them powerless. Those effects are permanent. He didn't have to execute them.
The acknowledgment by this new all-seeing character that Superman has never killed removes this stain from his history. Although it was an interesting period, seeing the Man of Steel deal with killing others, it took something away from the character. Superman should be able to find a better way, and killing those Kryptonians was absolutely anything but. Now, however, he's been restored to that point he was at before. He is the hero that everyone thought he was, even if it did take a major retcon. It's interesting, as Infinite Frontier, DC's latest reboot, restored all of DC's lost history. In theory, that would mean the execution of Zod, Quex-Ul and Zaora. The fact that it clearly doesn't, as stated here, shows how important it is that the character is not a killer. Not just in this story, but as a whole.