This whole idea of "us versus them" is an integral part of a lot of sports culture. That creation of artificial false dichotomies is exactly what sports is about, and exactly what society needs to avoid.
The question isn't academics versus athletes, it's inclusiveness versus divisiveness (or, worst case, the question of maximum long-term benefit to society). Both academics and athletes are capable of either, but at least in schools, one side is much more prominently divisive than the other.
I'm not sure society needs to avoid it. And even if it did, I'm not sure individual humans can.
Differentiating between things is a core functionality of the brain, and separating people into groups and categories is necessary to identify which decisions are correct or what actions to take in a given scenario. It becomes degenerate when this kind of divisiveness stops being "friendly competition" and starts being a feedback-loop of antagonistic rationalizations.
Even so, it is hard to be inclusive with people who aren't inclined to be inclusive. It's not something that you can achieve with just intent; it requires a community with the right infrastructure. And it is hard enough for individuals to control their own behavior that controlling community behavior is almost always intractable.
I'm not sure that it is inappropriately cynical to think "I'm just going to pick the side I like and criticize the one I don't. If the other side doesn't understand this and value it, then screw 'em."
The question isn't academics versus athletes, it's inclusiveness versus divisiveness (or, worst case, the question of maximum long-term benefit to society). Both academics and athletes are capable of either, but at least in schools, one side is much more prominently divisive than the other.