I listened to the full audio.
In a vacuum, when you say that 'baseball is so easy to understand that 1/3rd of the league is Dominican', it just doesn't come off well. He did follow it up by saying that it's because a lot of those kids do not have the same educational opportunities that many kids in other countries do have. He points out that if he said "1/3 of the league is from countries with economic hardships therefore education hurdles", it probably would not have been an issue. I'm not sure that completely exalts him because he's essentially saying the Dominican Republic is too impoverished to properly educate it's citizens. Even if that was a fairly accurate depiction, I'm not sure I would want to hear that if I was from that Country.
That said, I am not a Cowherd fan and do not watch him with enough frequency to make judgement on his character, but at a glance I do not believe Cowherd has prejudice and hate in his heart. Sometimes decent people say stupid things, and when you're on the air for four hours a day or whatever crazy amount he is, you are bound to eventually say something you regret; I know I would.
If ESPN were not actively looking to cut-costs with their top-end on-air talent, I wonder if they might have handled this slightly differently.