A lot of fans seem confused how there could be a war between the universes if Peter never existed. After all, wasn't he the whole reason Walter originally crossed over? And didn't his conversation with young Olivia cause Walternate to figure out about the Blue Universe? The answer to both questions is yes. But I think were still meant to infer that the war between the universes was inevitable.
In "Peter," Walter said Belly was always urging them to cross over to steal more technology. We can assume, therefore, that the two would have done so at some point regardless. Also, Walter alluded to a "mistake" in "The Day We Died," suggesting the first crossing may have been an unintended error.
Once you assume the crossing was inevitable, then so was Walternate's discovery of the Blue Universe. Indeed, it seems odd to think Walter would be able to discover the Red Universe while Walternate would remain oblivious to the Blue. At a minimum, he would have figured out what was up once his universe started collapsing. Also, we know Belly approached Walternate at some point, presumably to get more technology.
So, the war was inevitable, too, it was just a matter of time. By removing Peter from the timeline, however, the Observers made the conflict less personal between Walter and Walternate, setting the stage for their future cooperation.