Everything the heroes ever experience is an "alternate timeline" - all timelines are "alternate" to each other. The only thing that matters for the heroes is the timeline in which they themselves exist, though. Except when they have the luxury of making life happier for people in other timelines as well.
Which is more or less what this episode was about - the characters arguing whether they had the luxury.
In a typical grandfather "paradox", two timelines will keep flipflopping. If you go back to shoot your grandfather, you don't disappear because you were
born, once. But the guy who will go back to kill the grandfather will not be born now, so a timeline emerges where the grandfather lives, and the guy will be born and will go back to kill the grandfather. It's self-perpetuating and in no way paradoxical, and all that matters is whether the camera in the past follows the murderous-intent you, or a timeline where no murderous you was present and everything panned out just fine for your grandfather.
In "Children of Time", the camera happens to follow a bunch of heroes who vacillate between their intentions. Many of the Mirror Universe stories have the same theme: it doesn't really matter to the heroes, but they have the power to do good, so why not?