This is only an opinion based on knowing nothing else but some basic's about the high school experience.
High school prepares a young man to experience social, academic and some parts of the "world-of-things" all wrapped up in a somewhat controlled environment. Unless there's more to your son's environment that what's stated in your postings, I would suggest letting your son deal with the overall high school experience, come home and talk to you, then learn from the roads that you've traveled, then return to high school the next day and road-test your advice, sort of speak. If baseball is the only fly in the ointment, there's always summer ball and such - unless his high school ball carries over into all the summer leagues in your area.
I've seen the results of pulling a young man out of one school, just to satisfy a sport - it's not good for many... not all mind you... just enough of the sample population that I've seen and met. One of the biggest drawbacks that I've seen is the lack of social friendships outside the usual family and close friends... friends that either live next door, down the street and so forth.
So the big picture is worth sitting back and looking at with some time and patience, balancing the experiences of life in total. I sincerely wish you the best in this process. I've never had to deal with this as a father so I can only suggest from a different perspective.