There are two separate issues. As a general rule, prep schools are intended for students who need additional academic preparation before entering a SA. This can either be due to the fact they had weak h.s. prep or simply they want an even stronger background (i.e., improved study skills, more work in a particular course) to better prepare them for the rigors of an SA.
If the main issue is physical fitness, that can be more readily addressed outside of a prep-school environment. If self-motivation is an issue, I would suggest working with a personal trainer. The money spent on that will be much less than a prep school and can provide similar benefits from a physical/athletic standpoint.
Also, it's not clear whether your DD is applying this year or thinking of applying next year. If the latter, and her grades/scores are good, from a USNA standpoint, she's better off at a regular college vs. prep school. She can work on her athletics anywhere.