If you're worrying about a story arc lost due to your killings, don't worry. Abernathy Farm is not involved in any important story line whatsoever. You do, however, lose a couple of quests involving the settlers (one is a radiant one), and one "quest" where you turn in melons, but it is not that important.
However, if you want to revert your manslaughter to recover people in the farm (and potentially companion reputations), that is a completely different issue. In console versions of Fallout 4, there is no way of undoing your progress aside from reloading your previous save. Had it been a PC version, you could have used cheat codes to resurrect them and/or recover your reputation, but console versions don't have access to that UI. I'm sorry.
On a side note, if you badly needed cloth, concrete, fertilizer, leather, or wood, bear in mind that you lost Connie Abernathy, who sells these junks in a mass. It's not a big deal later on, since she is not the only vendor who sells such things.