I like that you are so passionate about stopping baseball players from distance running. Very odd but I can appreciate it.
As I tell the many pitchers that I have worked with and gone on to play in college and pro ball. Stick with the program. Adjust when necessary but be consistent with your throwing program, running (distance and sprint work), workouts, and stretch.
My talent got me noticed but the entire program (running included) kept me around and kept me healthy so that I could improve and develop my talent.
Parents and Players, let me know if you have any other pitching questions.