If the game flops, I don't think it'd be a direct result of the JonTron nonsense. Sure it'll have an impact on the sales, but I believe it'll be extremely minor. If you actually slog through the YookaLaylee hashtag on Twitter or any video on Youtube ranting about it, a large chunk of the people commenting negatively about Yooka-Laylee outright state that they weren't even interested in the game to begin with.
All-in-all, I think that if this game ends up selling poorly, it probably would've sold poorly without the JonTron drama. The effect it has on sales, for better or worse, is gonna be minuscule.