I think there is some confusion. The coach is in control - not your son. The whole - coach is going to have to understand and my son will not make any accommodations - routine is going to get him his choice of class time because he's going to be cut for being a difficult freshman or he's going to get a lot of FaceTime with the coach because he'll be right next to him on the bench after missing 75% of practices.
The correct way to handle this situation would be to have your son approach the coach and explain the situation. If the coach is a reasonable person he will say yes things changed, talk to this person and let's figure something out.
He can also say practice is at this time, figure it out. Which is wrong, but so is telling the coach; this is how things work, deal with it.
Your kid is a freshman, he has the most mobility he'll ever have in terms of what courses he can take - it's not like he's 110 credits in and specifically needs three more courses. Every other freshman regardless of extracurriculars is able to make their schedule and get courses within their major, it's possible.
I would also imagine if the entire team was told to block after 2 pm off they would all be running into this problem no?
Have him talk to the team captain, talk to the coach. Do not escalate this yourself, everything related to his college experience is on him. If you are footing the bill, you and your son work out an arrangement between you two, everything else related to school and baseball is for him to take care of. This should be a fixable situation, talk to an advisor in the athletic dept