While Nocturne certainly seems like a clear-cut villain, his motivations, from what he's hinted at, aren't entirely unreasonable. Here's the thing: what if he does have a good reason?
After all, he ONLY targeted Summoners and no one else, and a JoJ interview (of debatable canonicity at this point, but I digress) indicates that he truly despises Summoners, and not just because they're enslaving him as punishment for attempting to systematically eliminate them. While this could just be some sort of unfathomable alien hatred for powerful magic users, his threats indicate very human reasons for wanting to kill them. Put some thought into it, and it's quite possible that he has a very legitimate point.
After all, they've demonstrated some truly incredible lapses of judgment by way of enslaving other cosmic horrors and letting known war criminals, terrorists, amoral mercenaries, power-hungry sorcerers, openly malevolent undead, violent psychopaths, and other highly dangerous and/or unstable individuals get a free pass just by agreeing to work for them, and there's no small amount of indication that quite a few of the more powerful individuals in their employ are far too powerful for them to control, so what's to say that he wasn't trying to kill them because of how arrogant, myopic, idiotic, and flat-out morally bankrupt they generally are? The nightmares that plagued them could have very easily been the equivalent of warning shots; when they failed to heed them, he just cut to the chase and killed them. In fact, it's entirely possible that he's an extradimensional policeman of sorts who monitors the waking world through dreams for anything indicating a possible threat to reality, and that the Summoners just so happened to be a big enough threat to warrant lethal force.