Following the rules didn't help them. The rule was no templating tools that generate code. They didn't use that.
It simply seems like they had to deal with a school official who was too dumb to know what GitHub was and too egotistical to admit they might be wrong.
I actually dealt with something similar back in my high school days. I self-taught myself to program starting around age 10 or so. So by the time I was offered and took a "computer class" that had some programming in it in high school, I already knew what I was doing. Far better than the teacher in the class. Every project in the class I found very easy and did perfectly within the parameters requested, often time going way beyond the requirements. The teacher didn't like one bit that I was far exceeding her capabilities and the level expected and would find every excuse to mark me down. Her favorite excuse was to take issue with my comments (where I didn't explain every obvious line of code in verbose text). I barely passed the class.
After that, I changed my mind and decided I wouldn't study computer science in university, instead deciding to skip school altogether. Eventually did go to university after a gap year, but to study design instead. I was completely turned off from learning CS by this one teacher and it dramatically changed the course of life after. I did continue coding and ended up building some cool stuff, including a couple startups before switching to venture capital.
Hopefully for these kids it'll be a trigger for positive change too.