There were a lot of rule changes involving pitching as the game developed in the 1870s and 1880s. For instance, a batter was allowed to call for a high or low pitch for some time. The number of outside-the-strike-zone pitches needed for a walk dropped from eight (!) to the present day four. Foul balls weren't always strikes. And the mound was moved back from fifty feet to the present 60' 6" sometime in the early 1890s (I believe the first NL season with the present mound distance was 1893). Take your pick from any of those.
And don't forget the NL dropped four teams (Cleveland, Louisville, Washington, Baltimore) after the 1899 season. You have a massive butterfly right there if that didn't happen (although you'd have to do something fairly drastic to save the Cleveland Spiders: the 1899 edition of that team had a record of 20-134, a full sixteen wins fewer than the modern-day record worst team, the 1916 A's). What you might have is a few determined types who want to get baseball into Detroit, Milwaukee, and perhaps the Twin Cities and Buffalo who might force (don't know how) the NL into creating four new franchises so that the league becomes a sixteen team monster, and more or less has to split into two divisions.