That's the theory I've come to after the latest episode. It did not look in that fight like Nora was the object of the battle for either party.
Originally both Barry's parents lived and he didn't become The Flash till like 2020. Somehow in his time traveling adventures he and Eobard Thawne became enemies. Eobard didn't realize originally that he needed The Flash to exist to use his powers.
Eobard traveled back in time to kill Barry as a kid. Future Barry followed him to stop him but Nora would up being killed by accident. Eobard got stranded in the past, and from there on history plays out differently.