I don't feel they fully explored the ramifications of the plot they went with to stop the invasion. Basically the ending with Peter and Olivia in the field with their daughter, yeah, that wouldn't happen. Much of the first three seasons happened solely because of September's interference, and he would no longer exist given their plan to stop Observers from ever being created. Sad thing is I actually thought they took that into account when Walter was talking about having to lose Peter for their plan to work. I thought it was a callback to when Peter was sick as a child and died and the timeline would revert to that still being the case.
So yeah, large chunks of the shows mythology would be entirely rewritten based on their plan to stop the invasion, but of course they aren't going to end a show with that, they will give it the happy ending.