Zarya isn't a counter for genji, just a minor annoyance. The way Zaryas beam works, unless you have pinpoint accuracy and can keep it on him constantly (near impossible) you'll do not a lot, and he can just keep at a distance. The only minor counters to him are Winston, Mei, McCree and Roadhog. With Winston and Mei he can just dash away, McCree can plink away at him from a distance and stun him if he gets close, but McCree is not a hard counter, it's a pretty even match, roadhog you HAVE to land the hook. Truth is Genji can counter his counters which is what makes him so ridiculous.
At competitive play Genji isn't an issue, basically Genji is overpowered in high-level play because he's hard to hit and you can't shut him down quickly enough, in low-level play the Genjis are basically a detriment to their team, in competitive play the players are so accurate you can shut him down quickly because the players have godly aim, there is a "Genji gutter" which is somewhere between rank 60-80, where you're not good enough to counter his mobility but he's good enough to wreck your team with his ult.