But did he still interrupt Walternate in his experiment on the cure? If so, then the combination of interfering with Walternate and choosing not to interfere at Reiden Lake still is a net interference with the intention of destroying RedPeter. If not, then Walter would have no motive to cross, as Walternate could have made the appropriate adjustment to the serum.I don't see that September "made it so" - as September simply did nothing in this reality. All he did was Observe.
One of my half-baked theories is that Peter survived in his own world in the "base" reality, creating the machine with Walternate as the ultimate weapon in a hot war with the Blueverse (undertaken for reasons probably related to Walter & Bell). But destruction of the Blueverse caused the drawn-out destruction of the Redverse. The machine was rebuilt to send through the temporal wormhole, with one part containing an extract of Peter's memories to inform his counterpart in the next loop. But that part was either damaged or sabotaged (by rogue Observers? the Sam Weisses? Peter's "confusion" in TLSW is evidence that the memory overlay could have existed.) so that the cycle continued through an indefinite number of loops. At last, September deliberately interrupted Walternate in order to change Peter's upbringing and personality, creating a potential way out of the loop. He cast it as a mistake to his cohort to retain his position. The way out of the loop was Walter's choice of an alternative method of informing Peter of the consequences. The branch was created.
I'm still unsure about how the branch gave September the opportunity to change his action at Reiden Lake in 1985, but it probably has something to do with Walter's explanation of Emily's abilities: some traumatic events echo backward through time.