At the end of the day GitHub is a web app. I don’t think it’s worth complaining about unless it’s something like Wikipedia that stops working.
I see that GitHub now tries to become at the same time a social media for hacker-friendly people and some sort of super-CI server with automation. For sure these are good features. However I also see why people are sad that the old (and defining) functionalities stopped working without JS.(look at commit, browse the sources, read and submit issues / PR and code review). It saddens me a bit to often see working websites getting more and more complex, adding more and more features, probably to remain "fancy" and competitive.
For sure there is a discussion to be had about whether the addons that GitHub provides over and above being a server for a .git directory need JavaScript, but that feels like a different discussion than “it’s just a server for .git directories”