@Jen234 I think you've figured out what you need to do. A little advice on how to proceed with that....
Don't meet or correspond with the program director until you've calmed down a bit. These conversations do not need to be the heated "you slighted my kid" but rather "you offered a sale of services and we are not receiving what was advertised" conversations. It's a business and even though it's your kid, it's a business deal. You likely won't see your money back but you may be able to negotiate. Obviously, first try for a refund, show good faith and ask for a partial based on services/events you have paid for and have not received yet, something reasonable, good faith offer. I know it's hard to monetize your kid's losses. The other option would be to have your son be allowed to train there, I'm guessing there are private lessons at the facility? get private hitting lessons in lieu of practices etc. (I personally had success with this when my son first started playing TB at 11, we picked a team based out of a great facility not realizing there wasn't a full team and the field practice we had participated in was a 11/12 combined practice. It was a disaster, you can't play games, much less tournaments without a full team. We negotiated team fees be transferred to private lessons/cage access and offered to guest play with the incomplete team as long as his new team didn't have a tournament that weekend. It actually worked out great as we moved to a team we really liked but didn't have a facility so were out of luck when weather hit). Some of these baseball guys are just trying to keep a business afloat, they want to make it right but also need your money in their coffers.
It is likely the program director/owner likely has no idea what's going on at your team level and will apologize and offer to make it right. Unless he replaces the shortstop-dad coach, it won't happen. And if he does his core 9 will likely leave...