That's not fair.

I actually had a sorta similar situation when my son was in Middle School. That year he was diagnosised as having a severe learning disability in reading comprehension. His History teacher wanted to fail him in her class even after the diagnosis. I went above her to the Head of Learning Support and told him this was just not fair. The Head of Learning Support stuck up for my son and got the teacher to reverse her decision.
I would definitely go to the Principle or whoever you need to go to so that hopefully that will be changed for your son. It never hurts to ask. Keeping my fingers crossed that the school system does the right thing by your son.