The primary lesson to learn from Greco-Roman mythology is "Never swear anything by the River Styx." It never helps. Every time the gods do it, they always wind up regretting doing so. It invites disaster of one form or another, because it is the oath that no god ever dares to break.
What do your gods fear? What won't they do? If the gods can kill Atlanteans with a thought, at any time and across any distance, then the only thing that can really stop them from genociding the whole race in an instant is having a reason not to. It might be a law of some kind, or a limitation on their power, or just about any other factor. They might not be happy about it: in fact, the very reason that they must not kill all the Atlanteans might also be the reason that they're so angry. But they must have some reason to accept, if only grudgingly, that some Atlanteans must live.
The Atlanteans' role in their own survival, then, would involve setting up this situation. Once they've angered the gods, they probably don't have much time to maneuver into the proper position, so it needs to be something they could do quickly. It's possible that the Atlanteans might not finish the process in time to save everyone, which would explain why the gods were able to kill almost all of them: the gods' hands were not tied until the last possible moment.
Here's one possible scenario: the Atlanteans were a proud people, acknowledging the power of the gods but finding them unworthy of worship (in other words, not so much atheists as dystheists). The gods did not consider them enough of a threat to be worth noticing... until a day came when the Atlanteans built an "apotheosis machine" to give the power of the gods to one of their own number: essentially, to make a new god. The machine blew up in the process, destroying a large portion of their civilization, but the test subject removed unscathed, glowing with his new divinity.
This angered and terrified the gods, who sought retribution by killing every Atlantean they could. They were forbidden by ancient law to kill true believers of any true god, as a means of preventing religious war, but the Atlanteans' pride had led them away from true belief, so the law gave them no protection. Or at least, it gave them no protection until the prototype -the new god- formed a faith around himself.
Not many Atlanteans were willing to worship any god, not even the one they had made. For that, they perished at the hands of the other gods, and died spitting upon their "craven" brothers who would live on bended knee. But a few Atlanteans did survive, under the de facto protection of the prototype. Their god is a pariah among the other gods for his "artificial" origins, and the "cowardice" of the surviving Atlanteans has not been forgotten either, so they are pariahs among people. But the gods must not kill them, and so they are grudgingly left alone.