To the OP: this is where it can be extremely helpful to have a few very trusted advisors that can steer a kid in the correct direction. Often this can be a Travel Ball coach or a hitting/pitching instructor or a trusted friend who is a scout or college coach. Someone who can tell you guys the truth, even if the truth is tough to hear.
Either the kid is not a good fit at this particular D1, or just not D1 material at all. I like the JUCO route, because it can open up the recruiting again to D1's after a year or two and it can give time for further development.
It is important for this kid to understand that this sort of thing happens fairly frequently.