I honestly don't see a problem here. They decided to change a backend library for a non-essential system in their product. Most services don't ask for permission or make announcements when they make changes like this. The approach seemed to be, if things break, people will report it and we’ll fix it. While this may not be the best approach, the number of languages supported is too high for a person to check each one…
For many languages this is a significant and distracting degradation in the presentation.
I could understand GitHub removing highlighting completely because they feel speed is the overriding priority. That would be even faster than what they're doing now. Languages would look "plain" instead of "wrong". Not my first choice, but a reasonable choice.
The situation now is that they've replaced a library that had been handling highlighting thoroughly, with a variety of text-editor lexers that mostly are not. People like me who already contributed to Pygments, aren't feeling motivated to do this all over again for no good reason. So it seems likely the lexers will remain poor for quite a long time. Which is unfortunate.
Finally, at the time I wrote my blog post, I was speculating about the motivation because GitHub hadn't explained why, yet. Someone later did explain ("because speed") in the issue thread.