Academics should always be in play. Very few players will play past high school or college. All players will go out into the real world (God willing) once they graduate college. In the real world, nobody cares where you played college baseball if you don't have a solid academic record.
Academics should always come first, and sports should always come second. I have never agreed more with a TRHit post. Let me be a little clearer: if I'm a D1 coach, and I have a choice between an academically mediocre player with good skills and an academically exceptional player with above-average skills, I would probably pick the academically exceptional player. Why? Because he's more likely to be eligible; he can help the team. The academically mediocre player may or may not be eligible; if he is, he'll help the team more. If he isn't, he'll be a waste of a spot.