HOW strongly does HS coach feel about players playing summer with him? What is the summer season? How competitive is the HS travel program? Can he play travel afterward? Does he play other sports/football? Does he work with a P instructor? What year is he? What is your role in the relationship? You said he just started playing 3b... how much potential for improvement is there?
If HS coach feels very strongly about players participating in summer program, be very careful. Also, with the timing of most HS summer programs, travel can be worked in (maybe late summer/fall). If there is a summer travel team that will put him top of rotation, there is likely one that will do same in the fall. Since he hits well, has a good arm and is apparently targeting NAIA and D3, I wouldn't rule out the possibility of him making it as a position player ( with some defensive work and conditioning work). I am saying this without knowing what exactly is behind your thought that he will not get opportunities as 3B, so you likely have more insight there - if D is that bad, you could be right.
So I guess this is a long winded way of saying we don't have all the info and know the kid's situation as well as you but be careful with advising against the HS coach and try to find other solutions if necessary in regards to pitching.