Yeah, I don't think it was well thought out, but that's pretty much the Affinity system in a nutshell. It sucks you have no other saves. But let this be a lesson and take the old motto to heart: "Save early, save often, save in multiple slots."
In theory you could use the console commands to change things, but unless you both manually edit your Affinity and reverse one of the old Decisions you could run into trouble down the line since your game state is technically invalid. It might be faster to just blitz through the game over again and choose differently.
Or, as you say, wait until Episode 9 is close and play Seasons 1 and 2 over again to get ready.