I’d choose the academics and future opportunities over playing D3 baseball. You never know if you will actually get playing time at the D3 college. I know of a number of baseball players (half dozen) who are going to D2 or D3 schools in the middle of nowhere and hardly play. If my kid got into UMich or UCB or UNC CH or UTA I’d suggest there over a D3 without scholarship.
Now if the D3 school is somewhere like NYU or Pomona or WashU or Chicago, I’d suggest staying the course….