Okay so first of all there's no job that's going to require one from the program director.

Second of all, obviously don't use this person as reference anymore. You already had concerns about whether or not they were a reference that could be relied upon. I'm having trouble understanding why you even included them as a reference in the first place. Why did you think that was required?

Also it doesn't really matter how "in the right" you are. In the eyes of the employer.

From their perspective: Maybe you've been completely a victim and the bad reference is BS. Maybe there's legitimate reasons why the program director said what they said.

But any employer that gets a bad reference is probably just going to move on to another candidate for whom there is not a bad reference.