Good for you for placing an emphasis on academics. My son is graduating in a week and I have always pushed him (just a bit) in the academic area, having read on here when he was a freshman that there is more academic money available than athletic money. This is especially important if your son is not a "blue chip" recruit.
My son got more academic money than baseball money. He also got an additional scholarship from an outside source based on his academics. So, bottom line is that he's got about an 85% scholarship to a private school. He is saving us a huge amount of money because of studying hard in high school.
He took many AP/honors classes that boosted his grade point average. Each college recalculates the student's gpa based on their own standards. So for the University of CA schools he applied to he had over a 4.0. Colleges want to see that the student has challenged themselves. We saw many of sons friends this year that had high gpa's and didn't get into many of the colleges they applied to. It may have been because they didn't take the most rigorous course load available to them.
So, no you have not hurt your son's chances with baseball recruiters. Send me a private message if you want more details.