Although you say that you and Mom have "50/50 custody" you don't say whether this is under a court order, a written agreement, or just an informal arrangement. If you have a court order or judgment about custody, you need to review the part that describes LEGAL custody, and which says who gets to make what sorts of decision about the child. (That's what LEGAL custody is about: decision-making; PHYSICAL custody is who the child spends time with, where, and when).
If the judgment says you and Mom have joint legal custody, AND it says she is not permitted to start school enrollment without your agreement, then you can "un-enroll" your son. You should review the court order about custody with an experienced family law attorney to be clear on your rights and remedies.
I agree with my colleague, unless your custody order specifically gives you the right to have some say over educational matters, you may not have a leg to stand on. Making blanket claims that enrolling a child in the California school system is a peril will likely not resonate with a Judge.
Sign up to receive a 3-part series of useful information and advice about child custody law.