BaseballJoe's experience at Hopkins reminds me of one of the most important lessons I learned during my son's recruiting experience: The process is a "black box," and a lot of stuff happens that you can't understand and will never know the reasons for. Coaches will text your kid weekly for a couple of months, then ghost him for a while, then start texting again. Your son will be pursued avidly by three schools in one conference, but a fourth won't even respond to his emails (even though that fourth school is less competitive in baseball and academics that some of their fellow conference members who have shown interest). It can be frustrating (or infuriating), but you just have to roll with it. Sounds like BaseballJoe and his son did just that--they felt like they weren't "loved" at Hopkins, so they moved on.
If your son is still interested in Hopkins, then I think fenwaysouth's advice is good. It could be worth following up with Babb (who is great about answering emails and who I have always heard is a straight shooter). I also remember Babb saying when my son and I met with him some years ago that raising a GPA was difficult, but a player could always re-take a standardized test and potentially add a few points.