I’m actually not sure this would be as significant as it seems. Yes, the Rhydon matchup would be different, but my biggest problem with Water-Type move Zapdos in RBY would be that you become much worse into Exeggutor as a result of dropping Drill Peck. Thunder Wave + Agility, especially on lead Zapdos, is too important to drop IMO and while this is absolutely not a common pick, I have seen some posts over time, including one recently, that suggested Zapdos could try and use Toxic in the actual tier to, obviously not completely flip the matchup, but at least be able to do something to Rhydon. I would personally much rather be walled by Rhydon than walled by Exeggutor if I had to pick.
Edit: Of course, the pro-ban argument would be that you don’t know if Zapdos is going to be running Drill Peck, a Water move, or both in this hypothetical landscape, and this could lead to uncompetitive scenarios where a player wins because they happened to have the correct coverage move by chance.